diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/H5D.c | 72 | ||||
| -rw-r--r-- | src/H5S.c | 123 | ||||
| -rw-r--r-- | src/H5Sall.c | 755 | ||||
| -rw-r--r-- | src/H5Shyper.c | 5847 | ||||
| -rw-r--r-- | src/H5Spkg.h | 49 | ||||
| -rw-r--r-- | src/H5Spoint.c | 644 | ||||
| -rw-r--r-- | src/H5Sprivate.h | 111 | ||||
| -rw-r--r-- | src/H5Sselect.c | 1265 | ||||
| -rw-r--r-- | src/H5Tconv.c | 10 |
9 files changed, 2735 insertions, 6141 deletions
@@ -13,13 +13,13 @@ /* $Id$ */ #include "H5private.h" /* Generic Functions */ -#include "H5Iprivate.h" /* IDs */ #include "H5Dprivate.h" /* Dataset functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5FDprivate.h" /* File drivers */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Gprivate.h" /* Group headers */ #include "H5HLprivate.h" /* Name heap */ +#include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ #include "H5Oprivate.h" /* Object headers */ #include "H5Pprivate.h" /* Property lists */ @@ -70,11 +70,8 @@ H5FL_DEFINE_STATIC(H5D_t); /* Declare a free list to manage blocks of type conversion data */ H5FL_BLK_DEFINE_STATIC(type_conv); -/* Declare a free list to manage blocks of background conversion data */ -H5FL_BLK_DEFINE_STATIC(bkgr_conv); - -/* Declare a free list to manage blocks of fill conversion data */ -H5FL_BLK_DEFINE_STATIC(fill_conv); +/* Declare a free list to manage blocks of single datatype element data */ +H5FL_BLK_DEFINE(type_elem); /* Declare a free list to manage blocks of VL data */ H5FL_BLK_DEFINE_STATIC(vlen_vl_buf); @@ -1694,6 +1691,7 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, H5O_reset(H5O_FILL, &fill_prop); if(fill.buf && (NULL==H5O_copy(H5O_FILL, &fill, &fill_prop))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT,NULL,"unable to copy fill value"); + H5O_reset(H5O_FILL_NEW, &fill); /* Write old fill value */ if (fill_prop.buf && H5O_modify(&(new_dset->ent), H5O_FILL, 0, H5O_FLAG_CONSTANT, &fill_prop) < 0) @@ -2373,10 +2371,10 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from file to memory data space"); /* - * If there is no type conversion then try reading directly into the + * If there is no type conversion then read directly into the * application's buffer. This saves at least one mem-to-mem copy. */ - if (H5T_IS_NOOP(tpath) && sconv->read) { + if (H5T_IS_NOOP(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif @@ -2434,11 +2432,11 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, request_nelmts = target_size / MAX(src_type_size, dst_type_size); /* Figure out the strip mine size. */ - if ((sconv->f->init)(file_space, src_type_size, &file_iter)<0) + if (H5S_select_iter_init(file_space, src_type_size, &file_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); - if ((sconv->m->init)(mem_space, dst_type_size, &mem_iter)<0) + if (H5S_select_iter_init(mem_space, dst_type_size, &mem_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); - if ((sconv->m->init)(mem_space, dst_type_size, &bkg_iter)<0) + if (H5S_select_iter_init(mem_space, dst_type_size, &bkg_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); /* Sanity check elements in temporary buffer */ @@ -2468,7 +2466,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { /* Allocate background buffer */ H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); - if((bkg_buf=H5FL_BLK_ALLOC(bkgr_conv,(size_t)(request_nelmts*dst_type_size),0))==NULL) + if((bkg_buf=H5FL_BLK_ALLOC(type_conv,(size_t)(request_nelmts*dst_type_size),0))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); } /* end if */ @@ -2476,7 +2474,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, H5_CHECK_OVERFLOW(nelmts,hssize_t,hsize_t); for (smine_start=0; smine_start<(hsize_t)nelmts; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ - smine_nelmts = (sconv->f->avail)(file_space,&file_iter, + smine_nelmts = H5S_select_favail(file_space,&file_iter, MIN(request_nelmts, (nelmts-smine_start))); /* @@ -2489,7 +2487,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #endif /* Sanity check that space is allocated, then read data from it */ assert(dataset->layout.addr!=HADDR_UNDEF || efl.nused > 0); - n = (sconv->f->gath)(dataset->ent.file, &(dataset->layout), + n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), dc_plist, src_type_size, file_space, &file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/); @@ -2505,8 +2503,8 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif - n = (sconv->m->gath)(buf, dst_type_size, mem_space, &bkg_iter, - smine_nelmts, bkg_buf/*out*/); + n = H5S_select_mgath(buf, dst_type_size, mem_space, &bkg_iter, + smine_nelmts, dxpl_id, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].bkg_timer), &timer); sconv->stats[1].bkg_nbytes += n * dst_type_size; @@ -2528,8 +2526,8 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif - status = (sconv->m->scat)(tconv_buf, dst_type_size, mem_space, - &mem_iter, smine_nelmts, buf/*out*/); + status = H5S_select_mscat(tconv_buf, dst_type_size, mem_space, + &mem_iter, smine_nelmts, dxpl_id, buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].scat_timer), &timer); sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size; @@ -2566,7 +2564,7 @@ done: if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME)) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) - H5FL_BLK_FREE(bkgr_conv,bkg_buf); + H5FL_BLK_FREE(type_conv,bkg_buf); if (free_this_space) H5S_close(free_this_space); FUNC_LEAVE(ret_value); @@ -2803,10 +2801,10 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from memory to file data space"); /* - * If there is no type conversion then try writing directly into the + * If there is no type conversion then write directly from the * application's buffer. This saves at least one mem-to-mem copy. */ - if (H5T_IS_NOOP(tpath) && sconv->write) { + if (H5T_IS_NOOP(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif @@ -2865,11 +2863,11 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); /* Figure out the strip mine size. */ - if ((sconv->f->init)(file_space, dst_type_size, &file_iter)<0) + if (H5S_select_iter_init(file_space, dst_type_size, &file_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); - if ((sconv->m->init)(mem_space, src_type_size, &mem_iter)<0) + if (H5S_select_iter_init(mem_space, src_type_size, &mem_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); - if ((sconv->f->init)(file_space, dst_type_size, &bkg_iter)<0) + if (H5S_select_iter_init(file_space, dst_type_size, &bkg_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); /* @@ -2899,7 +2897,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { /* Allocate background buffer */ H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); - if((bkg_buf=H5FL_BLK_ALLOC(bkgr_conv,(size_t)(request_nelmts*dst_type_size),1))==NULL) + if((bkg_buf=H5FL_BLK_ALLOC(type_conv,(size_t)(request_nelmts*dst_type_size),1))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); } /* end if */ @@ -2907,7 +2905,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, H5_CHECK_OVERFLOW(nelmts,hssize_t,hsize_t); for (smine_start=0; smine_start<(hsize_t)nelmts; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ - smine_nelmts = (sconv->f->avail)(file_space,&file_iter, + smine_nelmts = H5S_select_favail(file_space,&file_iter, MIN(request_nelmts, (nelmts-smine_start))); /* @@ -2918,8 +2916,8 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif - n = (sconv->m->gath)(buf, src_type_size, mem_space, &mem_iter, - smine_nelmts, tconv_buf/*out*/); + n = H5S_select_mgath(buf, src_type_size, mem_space, &mem_iter, + smine_nelmts, dxpl_id, tconv_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].gath_timer), &timer); sconv->stats[0].gath_nbytes += n * src_type_size; @@ -2932,7 +2930,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif - n = (sconv->f->gath)(dataset->ent.file, &(dataset->layout), + n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), dc_plist, dst_type_size, file_space, &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); @@ -2958,7 +2956,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif - status = (sconv->f->scat)(dataset->ent.file, &(dataset->layout), + status = H5S_select_fscat(dataset->ent.file, &(dataset->layout), dc_plist, dst_type_size, file_space, &file_iter, smine_nelmts, dxpl_id, tconv_buf); @@ -3005,7 +3003,7 @@ done: if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME)) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) - H5FL_BLK_FREE(bkgr_conv,bkg_buf); + H5FL_BLK_FREE(type_conv,bkg_buf); if (free_this_space) H5S_close(free_this_space); @@ -3244,7 +3242,7 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space) bufsize = ptsperbuf*fill.size; /* Allocate temporary buffer */ - if ((buf=H5FL_BLK_ALLOC(fill_conv,bufsize,0))==NULL) + if ((buf=H5FL_BLK_ALLOC(type_conv,bufsize,0))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer"); /* Fill the buffer with the fill value */ @@ -3291,7 +3289,7 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space) done: if (buf) - H5FL_BLK_FREE(fill_conv,buf); + H5FL_BLK_FREE(type_conv,buf); FUNC_LEAVE(ret_value); } @@ -3765,7 +3763,7 @@ H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_t /* Get the maximum buffer size needed and allocate it */ buf_size=MAX(src_type_size,dst_type_size); - if (NULL==(tconv_buf = H5MM_malloc (buf_size)) || NULL==(bkg_buf = H5MM_calloc(buf_size))) + if (NULL==(tconv_buf = H5FL_BLK_ALLOC(type_elem,buf_size,0)) || NULL==(bkg_buf = H5FL_BLK_ALLOC(type_elem,buf_size,1))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed"); /* Copy the user's data into the buffer for conversion */ @@ -3794,11 +3792,11 @@ H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_t done: if (tconv_buf) - H5MM_xfree(tconv_buf); + H5FL_BLK_FREE(type_elem,tconv_buf); if (bkg_buf) - H5MM_xfree(bkg_buf); + H5FL_BLK_FREE(type_elem,bkg_buf); FUNC_LEAVE (ret_value); -} /* H5Dfill() */ +} /* H5D_fill() */ /*-------------------------------------------------------------------------- @@ -16,12 +16,12 @@ #define _H5S_IN_H5S_C #include "H5private.h" /* Generic Functions */ -#include "H5Iprivate.h" /* ID Functions */ #include "H5Eprivate.h" /* Error handling */ +#include "H5Iprivate.h" /* ID Functions */ #include "H5FLprivate.h" /* Free Lists */ #include "H5MMprivate.h" /* Memory Management functions */ #include "H5Oprivate.h" /* object headers */ -#include "H5Spkg.h" /* Data-space functions */ +#include "H5Spkg.h" /* Dataspace functions */ /* Local static function prototypes */ @@ -31,9 +31,12 @@ static int interface_initialize_g = 0; static herr_t H5S_init_interface(void); -/* Tables of file and memory conversion information */ -static const H5S_fconv_t *H5S_fconv_g[H5S_SEL_N]; -static const H5S_mconv_t *H5S_mconv_g[H5S_SEL_N]; +#ifdef H5S_DEBUG +/* Names of the selection names, for debugging */ +static const char *H5S_sel_names[]={ + "none", "point", "hyperslab", "all" +}; +#endif /* H5S_DEBUG */ /* The path table, variable length */ static H5S_conv_t **H5S_conv_g = NULL; @@ -83,14 +86,6 @@ H5S_init_interface(void) "unable to initialize interface"); } - /* Register space conversion functions */ - if (H5S_register(H5S_SEL_POINTS, H5S_POINT_FCONV, H5S_POINT_MCONV)<0 || - H5S_register(H5S_SEL_ALL, H5S_ALL_FCONV, H5S_ALL_MCONV) <0 || - H5S_register(H5S_SEL_HYPERSLABS, H5S_HYPER_FCONV, H5S_HYPER_MCONV) <0) { - HRETURN_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, - "unable to register one or more conversion functions"); - } - #ifdef H5_HAVE_PARALLEL { /* Allow MPI buf-and-file-type optimizations? */ @@ -175,7 +170,7 @@ H5S_term_interface(void) /* Summary */ sprintf(buf, "%s %c %s", - path->m->name, 0==j?'>':'<', path->f->name); + H5S_sel_names[path->mtype], 0==j?'>':'<', H5S_sel_names[path->ftype]); fprintf(H5DEBUG(S), " %-16s\n", buf); /* Gather */ @@ -266,9 +261,8 @@ H5S_term_interface(void) H5I_destroy_group(H5I_DATASPACE); /* Clear/free conversion table */ - HDmemset(H5S_fconv_g, 0, sizeof(H5S_fconv_g)); - HDmemset(H5S_mconv_g, 0, sizeof(H5S_mconv_g)); - for (i=0; i<H5S_nconv_g; i++) H5MM_xfree(H5S_conv_g[i]); + for (i=0; i<H5S_nconv_g; i++) + H5MM_xfree(H5S_conv_g[i]); H5S_conv_g = H5MM_xfree(H5S_conv_g); H5S_nconv_g = H5S_aconv_g = 0; @@ -282,46 +276,6 @@ H5S_term_interface(void) } -/*------------------------------------------------------------------------- - * Function: H5S_register - * - * Purpose: Adds information about a data space conversion to the space - * conversion table. A space conversion has two halves: the - * half that copies data points between application memory and - * the type conversion array, and the half that copies points - * between the type conversion array and the file. Both halves - * are required. - * - * Note: The conversion table will contain pointers to the file and - * memory conversion info. The FCONV and MCONV arguments are - * not copied. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Tuesday, August 11, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -herr_t -H5S_register(H5S_sel_type cls, const H5S_fconv_t *fconv, - const H5S_mconv_t *mconv) -{ - FUNC_ENTER_NOAPI(H5S_register, FAIL); - - assert(cls>=0 && cls<H5S_SEL_N); - assert(fconv); - assert(mconv); - - H5S_fconv_g[cls] = fconv; - H5S_mconv_g[cls] = mconv; - - FUNC_LEAVE(SUCCEED); -} - - /*-------------------------------------------------------------------------- NAME H5S_create @@ -1514,7 +1468,9 @@ H5S_conv_t * H5S_find (const H5S_t *mem_space, const H5S_t *file_space, unsigned flags) { H5S_conv_t *path; /* Space conversion path */ +#ifdef H5_HAVE_PARALLEL htri_t opt; /* Flag whether a selection is optimizable */ +#endif /* H5_HAVE_PARALLEL */ size_t i; /* Index variable */ FUNC_ENTER_NOAPI(H5S_find, NULL); @@ -1537,8 +1493,8 @@ H5S_find (const H5S_t *mem_space, const H5S_t *file_space, unsigned flags) * If so then return a pointer to that entry. */ for (i=0; i<H5S_nconv_g; i++) { - if (H5S_conv_g[i]->f->type==file_space->select.type && - H5S_conv_g[i]->m->type==mem_space->select.type) { + if (H5S_conv_g[i]->ftype==file_space->select.type && + H5S_conv_g[i]->mtype==mem_space->select.type) { #ifdef H5_HAVE_PARALLEL /* @@ -1555,22 +1511,8 @@ H5S_find (const H5S_t *mem_space, const H5S_t *file_space, unsigned flags) } /* end if */ else { #endif /* H5_HAVE_PARALLEL */ - /* - * Check if we can set direct "all" read/write functions - */ - opt=H5S_all_opt_possible(mem_space,file_space,flags); - if(opt==FAIL) - HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, NULL, "invalid check for contiguous dataspace "); - - /* Check if we can use the optimized "all" I/O routines */ - if(opt==TRUE) { - H5S_conv_g[i]->read = H5S_all_read; - H5S_conv_g[i]->write = H5S_all_write; - } /* end if */ - else { - H5S_conv_g[i]->read = NULL; - H5S_conv_g[i]->write = NULL; - } /* end else */ + H5S_conv_g[i]->read = H5S_select_read; + H5S_conv_g[i]->write = H5S_select_write; #ifdef H5_HAVE_PARALLEL } /* end else */ #endif /* H5_HAVE_PARALLEL */ @@ -1580,21 +1522,14 @@ H5S_find (const H5S_t *mem_space, const H5S_t *file_space, unsigned flags) } /* - * The path wasn't found. Do we have enough information to create a new - * path? - */ - if (NULL==H5S_fconv_g[file_space->select.type] || NULL==H5S_mconv_g[mem_space->select.type]) - HRETURN_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, NULL, "unable to convert between data space selections"); - - /* - * Create a new path. + * The path wasn't found. Create a new path. */ if (NULL==(path = H5MM_calloc(sizeof(*path)))) HRETURN_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for data space conversion path"); /* Initialize file & memory conversion functions */ - path->f = H5S_fconv_g[file_space->select.type]; - path->m = H5S_mconv_g[mem_space->select.type]; + path->ftype = file_space->select.type; + path->mtype = mem_space->select.type; #ifdef H5_HAVE_PARALLEL /* @@ -1611,22 +1546,8 @@ H5S_find (const H5S_t *mem_space, const H5S_t *file_space, unsigned flags) } /* end if */ else { #endif /* H5_HAVE_PARALLEL */ - /* - * Check if we can set direct "all" read/write functions - */ - opt=H5S_all_opt_possible(mem_space,file_space,flags); - if(opt==FAIL) - HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, NULL, "invalid check for contiguous dataspace "); - - /* Check if we can use the optimized "all" I/O routines */ - if(opt==TRUE) { - path->read = H5S_all_read; - path->write = H5S_all_write; - } /* end if */ - else { - path->read = NULL; - path->write = NULL; - } /* end else */ + path->read = H5S_select_read; + path->write = H5S_select_write; #ifdef H5_HAVE_PARALLEL } /* end else */ #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5Sall.c b/src/H5Sall.c index 9a4d80d..6b975d9 100644 --- a/src/H5Sall.c +++ b/src/H5Sall.c @@ -10,56 +10,17 @@ #define H5S_PACKAGE /*suppress error about including H5Spkg */ -#include "H5private.h" -#include "H5Dprivate.h" -#include "H5Eprivate.h" -#include "H5Iprivate.h" -#include "H5Spkg.h" -#include "H5Tprivate.h" /* Datatypes */ -#include "H5Vprivate.h" +#include "H5private.h" /* Generic Functions */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5Iprivate.h" /* ID Functions */ +#include "H5Spkg.h" /* Dataspace functions */ +#include "H5Vprivate.h" /* Vector functions */ /* Interface initialization */ #define PABLO_MASK H5Sall_mask #define INTERFACE_INIT NULL static int interface_initialize_g = 0; -static herr_t H5S_all_init (const H5S_t *space, size_t elmt_size, H5S_sel_iter_t *iter); -static hsize_t H5S_all_favail (const H5S_t *space, const H5S_sel_iter_t *iter, - hsize_t max); -static hsize_t H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, - H5S_sel_iter_t *file_iter, hsize_t nelmts, - hid_t dxpl_id, void *buf/*out*/); -static herr_t H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, - H5S_sel_iter_t *file_iter, hsize_t nelmts, - hid_t dxpl_id, const void *buf); -static hsize_t H5S_all_mgath (const void *_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *_tconv_buf/*out*/); -static herr_t H5S_all_mscat (const void *_tconv_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *_buf/*out*/); - -const H5S_fconv_t H5S_ALL_FCONV[1] = {{ - "all", /*name */ - H5S_SEL_ALL, /*selection type */ - H5S_all_init, /*initialize */ - H5S_all_favail, /*available */ - H5S_all_fgath, /*gather */ - H5S_all_fscat, /*scatter */ -}}; - -const H5S_mconv_t H5S_ALL_MCONV[1] = {{ - "all", /*name */ - H5S_SEL_ALL, /*selection type */ - H5S_all_init, /*initialize */ - H5S_all_mgath, /*gather */ - H5S_all_mscat, /*scatter */ -}}; - /*------------------------------------------------------------------------- * Function: H5S_all_init @@ -75,7 +36,7 @@ const H5S_mconv_t H5S_ALL_MCONV[1] = {{ * *------------------------------------------------------------------------- */ -static herr_t +herr_t H5S_all_init (const H5S_t *space, size_t UNUSED elmt_size, H5S_sel_iter_t *sel_iter) { FUNC_ENTER_NOAPI(H5S_all_init, FAIL); @@ -110,7 +71,7 @@ H5S_all_init (const H5S_t *space, size_t UNUSED elmt_size, H5S_sel_iter_t *sel_i * *------------------------------------------------------------------------- */ -static hsize_t +hsize_t H5S_all_favail (const H5S_t * UNUSED space, const H5S_sel_iter_t *sel_iter, hsize_t max) { FUNC_ENTER_NOAPI(H5S_all_favail, 0); @@ -123,532 +84,6 @@ H5S_all_favail (const H5S_t * UNUSED space, const H5S_sel_iter_t *sel_iter, hsiz } /* H5S_all_favail() */ -/*------------------------------------------------------------------------- - * Function: H5S_all_fgath - * - * Purpose: Gathers data points from file F and accumulates them in the - * type conversion buffer BUF. The LAYOUT argument describes - * how the data is stored on disk and EFL describes how the data - * is organized in external files. ELMT_SIZE is the size in - * bytes of a datum which this function treats as opaque. - * FILE_SPACE describes the data space of the dataset on disk - * and the elements that have been selected for reading (via - * hyperslab, etc). This function will copy at most NELMTS - * elements. - * - * Return: Success: Number of elements copied. - * - * Failure: 0 - * - * Programmer: Quincey Koziol - * Tuesday, June 16, 1998 - * - * Modifications: - * Robb Matzke, 1999-08-03 - * The data transfer properties are passed by ID since that's - * what the virtual file layer needs. - *------------------------------------------------------------------------- - */ -static hsize_t -H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, - size_t elmt_size, const H5S_t *file_space, - H5S_sel_iter_t *file_iter, hsize_t nelmts, hid_t dxpl_id, - void *buf/*out*/) -{ - hsize_t actual_bytes; /* The actual number of bytes to read */ - hsize_t buf_off; /* Dataset offset for copying memory */ - - FUNC_ENTER_NOAPI(H5S_all_fgath, 0); - - /* Check args */ - assert (f); - assert (layout); - assert (elmt_size>0); - assert (file_space); - assert (file_iter); - assert (nelmts>0); - assert (buf); - - /* Set the offset in the dataset and the number of bytes to read */ - buf_off=file_iter->all.offset*elmt_size; - actual_bytes=elmt_size*nelmts; - - /* - * Read piece from file. - */ - H5_CHECK_OVERFLOW(actual_bytes,hsize_t,size_t); - if (H5F_seq_read(f, dxpl_id, layout, dc_plist, file_space, - elmt_size, (size_t)actual_bytes, buf_off, buf/*out*/)<0) { - HRETURN_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); - } - - /* Advance iterator */ - file_iter->all.elmt_left-=nelmts; - file_iter->all.offset+=nelmts; - - FUNC_LEAVE (nelmts); -} /* H5S_all_fgath() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_all_fscat - * - * Purpose: Scatters dataset elements from the type conversion buffer BUF - * to the file F where the data points are arranged according to - * the file data space FILE_SPACE and stored according to - * LAYOUT and EFL. Each element is ELMT_SIZE bytes. - * The caller is requesting that NELMTS elements are copied. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Tuesday, June 16, 1998 - * - * Modifications: - * Robb Matzke, 1999-08-03 - * The data transfer properties are passed by ID since that's - * what the virtual file layer needs. - *------------------------------------------------------------------------- - */ -static herr_t -H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, H5S_sel_iter_t *file_iter, - hsize_t nelmts, hid_t dxpl_id, const void *buf) -{ - hsize_t actual_bytes; /* The actual number of bytes to write */ - hsize_t buf_off; /* Dataset offset for copying memory */ - - FUNC_ENTER_NOAPI(H5S_all_fscat, FAIL); - - /* Check args */ - assert (f); - assert (layout); - assert (elmt_size>0); - assert (file_space); - assert (file_iter); - assert (nelmts>0); - assert (buf); - - /* Set the offset in the dataset and the number of bytes to write */ - buf_off=file_iter->all.offset*elmt_size; - actual_bytes=elmt_size*nelmts; - - /* - * Write piece from file. - */ - H5_CHECK_OVERFLOW(actual_bytes,hsize_t,size_t); - if (H5F_seq_write(f, dxpl_id, layout, dc_plist, file_space, - elmt_size, (size_t)actual_bytes, buf_off, buf/*out*/)<0) { - HRETURN_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); - } - - /* Advance iterator */ - file_iter->all.elmt_left-=nelmts; - file_iter->all.offset+=nelmts; - - FUNC_LEAVE (SUCCEED); -} /* H5S_all_fscat() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_all_mgath - * - * Purpose: Gathers dataset elements from application memory BUF and - * copies them into the data type conversion buffer TCONV_BUF. - * Each element is ELMT_SIZE bytes and arranged in application - * memory according to MEM_SPACE. - * The caller is requesting that at most NELMTS be gathered. - * - * Return: Success: Number of elements copied. - * - * Failure: 0 - * - * Programmer: Quincey Koziol - * Tuesday, June 16, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hsize_t -H5S_all_mgath (const void *_buf, size_t elmt_size, - const H5S_t UNUSED *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *tconv_buf/*out*/) -{ - const uint8_t *buf=(const uint8_t*)_buf; /* Get local copies for address arithmetic */ - hsize_t actual_bytes; /* The actual number of bytes to read */ - - FUNC_ENTER_NOAPI(H5S_all_mgath, 0); - - /* Check args */ - assert (buf); - assert (elmt_size>0); - assert (mem_space && H5S_SEL_ALL==mem_space->select.type); - assert (mem_iter); - assert (nelmts>0); - assert (tconv_buf); - - /* Set the offset in the dataset and the number of bytes to read */ - buf += mem_iter->all.offset*elmt_size; - actual_bytes=elmt_size*nelmts; - - /* "read" in the bytes from the source (buf) to the destination (tconv_buf) */ - H5_CHECK_OVERFLOW(actual_bytes,hsize_t,size_t); - HDmemcpy(tconv_buf,buf,(size_t)actual_bytes); - - /* Advance iterator */ - mem_iter->all.elmt_left-=nelmts; - mem_iter->all.offset+=nelmts; - - FUNC_LEAVE (nelmts); -} /* H5S_all_mgath() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_all_mscat - * - * Purpose: Scatters NELMTS data points from the type conversion buffer - * TCONV_BUF to the application buffer BUF. Each element is - * ELMT_SIZE bytes and they are organized in application memory - * according to MEM_SPACE. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Wednesday, June 17, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static herr_t -H5S_all_mscat (const void *tconv_buf, size_t elmt_size, - const H5S_t UNUSED *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *_buf/*out*/) -{ - uint8_t *buf=(uint8_t *)_buf; - hsize_t actual_bytes; /* The actual number of bytes to write */ - - FUNC_ENTER_NOAPI(H5S_all_mscat, FAIL); - - /* Check args */ - assert (tconv_buf); - assert (elmt_size>0); - assert (mem_space && H5S_SEL_ALL==mem_space->select.type); - assert (mem_iter); - assert (nelmts>0); - assert (buf); - - /* Set the offset in the dataset and the number of bytes to write */ - buf += mem_iter->all.offset*elmt_size; - actual_bytes=elmt_size*nelmts; - - /* "write" the bytes from the source (tconv_buf) to the destination (buf) */ - H5_CHECK_OVERFLOW(actual_bytes,hsize_t,size_t); - HDmemcpy(buf,tconv_buf,(size_t)actual_bytes); - - /* Advance iterator */ - mem_iter->all.elmt_left-=nelmts; - mem_iter->all.offset+=nelmts; - - FUNC_LEAVE (SUCCEED); -} - - -/*------------------------------------------------------------------------- - * Function: H5S_all_opt_possible - * - * Purpose: Checks if an direct I/O transfer is possible between memory and - * the file. - * - * Return: Success: Non-negative: TRUE or FALSE - * Failure: Negative - * - * Programmer: Quincey Koziol - * Wednesday, April 3, 2002 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -htri_t -H5S_all_opt_possible( const H5S_t *mem_space, const H5S_t *file_space, const unsigned UNUSED flags) -{ - htri_t c1,c2; /* Flags whether a selection is optimizable */ - htri_t ret_value=TRUE; - - FUNC_ENTER_NOAPI(H5S_all_opt_possible, FAIL); - - /* Check args */ - assert(mem_space); - assert(file_space); - - /* Check whether these are both simple dataspaces */ - if (H5S_SIMPLE!=mem_space->extent.type || H5S_SIMPLE!=file_space->extent.type) - HGOTO_DONE(FALSE); - - /* Check whether both selections are single blocks */ - c1=H5S_select_single(file_space); - c2=H5S_select_single(mem_space); - if(c1==FAIL || c2==FAIL) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "invalid check for single selection blocks"); - if(c1==FALSE || c2==FALSE) - HGOTO_DONE(FALSE); - - /* Check whether the shape of each block is the same */ - c1=H5S_select_shape_same(mem_space,file_space); - if(c1==FAIL) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "invalid check for selection blocks same"); - if(c1==FALSE) - HGOTO_DONE(FALSE); - -done: - FUNC_LEAVE(ret_value); -} /* H5S_all_opt_possible() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_all_read - * - * Purpose: Reads directly from file into application memory if possible. - * - * Return: Success: Non-negative. If data was read directly then - * MUST_CONVERT is set to zero, otherwise - * MUST_CONVERT is set to non-zero. - * - * Failure: Negative. Return value of MUST_CONVERT is - * undefined. - * - * Programmer: Robb Matzke - * Thursday, April 22, 1999 - * - * Modifications: - * Quincey Koziol, 1999-05-25 - * Modified to allow contiguous hyperslabs to be written out. - * - * Robb Matzke, 1999-08-03 - * The data transfer properties are passed by ID since that's - * what the virtual file layer needs. - *------------------------------------------------------------------------- - */ -herr_t -H5S_all_read(H5F_t *f, const H5O_layout_t *layout, H5P_genplist_t *dc_plist, - size_t elmt_size, const H5S_t *file_space, - const H5S_t *mem_space, hid_t dxpl_id, void *_buf/*out*/) -{ - H5S_hyper_span_t *file_span=NULL,*mem_span=NULL; /* Hyperslab span node */ - char *buf=(char*)_buf; /* Get pointer to buffer */ - hsize_t file_elmts; /* Number of elements in each dimension of selection */ - hssize_t file_off,mem_off; /* Offset (in elements) of selection */ - hsize_t mem_size[H5O_LAYOUT_NDIMS]; /* Size of memory buffer */ - hsize_t size[H5O_LAYOUT_NDIMS]; /* Size of selection */ - hssize_t file_offset[H5O_LAYOUT_NDIMS]; /* Offset of selection in file */ - hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /* Offset of selection in memory */ - unsigned u; /* Index variable */ - herr_t ret_value=SUCCEED; - - FUNC_ENTER_NOAPI(H5S_all_read, FAIL); - - /* Get information about memory and file */ - for (u=0; u<mem_space->extent.u.simple.rank; u++) { - switch(mem_space->select.type) { - case H5S_SEL_HYPERSLABS: - /* Check for a "regular" hyperslab selection */ - if(mem_space->select.sel_info.hslab.diminfo != NULL) { - mem_off=mem_space->select.sel_info.hslab.diminfo[u].start; - } /* end if */ - else { - mem_off=mem_span->low; - mem_span=mem_span->down->head; - } /* end else */ - mem_off+=mem_space->select.offset[u]; - break; - - case H5S_SEL_ALL: - mem_off=0; - break; - - case H5S_SEL_POINTS: - mem_off=mem_space->select.sel_info.pnt_lst->head->pnt[u] - +mem_space->select.offset[u]; - break; - - default: - assert(0 && "Invalid selection type!"); - } /* end switch */ - - switch(file_space->select.type) { - case H5S_SEL_HYPERSLABS: - /* Check for a "regular" hyperslab selection */ - if(file_space->select.sel_info.hslab.diminfo != NULL) { - file_elmts=file_space->select.sel_info.hslab.diminfo[u].block; - file_off=file_space->select.sel_info.hslab.diminfo[u].start; - } /* end if */ - else { - file_elmts=(file_span->high-file_span->low)+1; - file_off=file_span->low; - file_span=file_span->down->head; - } /* end else */ - file_off+=file_space->select.offset[u]; - break; - - case H5S_SEL_ALL: - file_elmts=file_space->extent.u.simple.size[u]; - file_off=0; - break; - - case H5S_SEL_POINTS: - file_elmts=1; - file_off=file_space->select.sel_info.pnt_lst->head->pnt[u] - +file_space->select.offset[u]; - break; - - default: - assert(0 && "Invalid selection type!"); - } /* end switch */ - - mem_size[u]=mem_space->extent.u.simple.size[u]; - size[u] = file_elmts; - file_offset[u] = file_off; - mem_offset[u] = mem_off; - } - mem_size[u]=elmt_size; - size[u] = elmt_size; - file_offset[u] = 0; - mem_offset[u] = 0; - - /* Read data from the file */ - if (H5F_arr_read(f, dxpl_id, layout, dc_plist, size, - mem_size, mem_offset, file_offset, buf/*out*/)<0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read data from the file"); - -done: - FUNC_LEAVE(ret_value); -} /* end H5S_all_read() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_all_write - * - * Purpose: Writes data directly to the file if possible. - * - * Return: Success: Non-negative. If data was written directly - * then MUST_CONVERT is set to zero, otherwise - * MUST_CONVERT is set to non-zero. - * - * Failure: Negative. Return value of MUST_CONVERT is - * undefined. - * - * Programmer: Robb Matzke - * Wednesday, April 21, 1999 - * - * Modifications: - * Quincey Koziol, 1999-05-25 - * Modified to allow contiguous hyperslabs to be written out. - * - * Robb Matzke, 1999-08-03 - * The data transfer properties are passed by ID since that's - * what the virtual file layer needs. - *------------------------------------------------------------------------- - */ -herr_t -H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout, H5P_genplist_t *dc_plist, - size_t elmt_size, const H5S_t *file_space, - const H5S_t *mem_space, hid_t dxpl_id, const void *_buf) -{ - H5S_hyper_span_t *file_span=NULL,*mem_span=NULL; /* Hyperslab span node */ - const char *buf=(const char*)_buf; /* Get pointer to buffer */ - hsize_t file_elmts; /* Number of elements in each dimension of selection */ - hssize_t file_off,mem_off; /* Offset (in elements) of selection */ - hsize_t mem_size[H5O_LAYOUT_NDIMS]; /* Size of memory buffer */ - hsize_t size[H5O_LAYOUT_NDIMS]; /* Size of selection */ - hssize_t file_offset[H5O_LAYOUT_NDIMS]; /* Offset of selection in file */ - hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /* Offset of selection in memory */ - unsigned u; /* Index variable */ - herr_t ret_value=SUCCEED; - - FUNC_ENTER_NOAPI(H5S_all_write, FAIL); - - /* Get information about memory and file */ - for (u=0; u<mem_space->extent.u.simple.rank; u++) { - switch(mem_space->select.type) { - case H5S_SEL_HYPERSLABS: - /* Check for a "regular" hyperslab selection */ - if(mem_space->select.sel_info.hslab.diminfo != NULL) { - mem_off=mem_space->select.sel_info.hslab.diminfo[u].start; - } /* end if */ - else { - mem_off=mem_span->low; - mem_span=mem_span->down->head; - } /* end else */ - mem_off+=mem_space->select.offset[u]; - break; - - case H5S_SEL_ALL: - mem_off=0; - break; - - case H5S_SEL_POINTS: - mem_off=mem_space->select.sel_info.pnt_lst->head->pnt[u] - +mem_space->select.offset[u]; - break; - - default: - assert(0 && "Invalid selection type!"); - } /* end switch */ - - switch(file_space->select.type) { - case H5S_SEL_HYPERSLABS: - /* Check for a "regular" hyperslab selection */ - if(file_space->select.sel_info.hslab.diminfo != NULL) { - file_elmts=file_space->select.sel_info.hslab.diminfo[u].block; - file_off=file_space->select.sel_info.hslab.diminfo[u].start; - } /* end if */ - else { - file_elmts=(file_span->high-file_span->low)+1; - file_off=file_span->low; - file_span=file_span->down->head; - } /* end else */ - file_off+=file_space->select.offset[u]; - break; - - case H5S_SEL_ALL: - file_elmts=file_space->extent.u.simple.size[u]; - file_off=0; - break; - - case H5S_SEL_POINTS: - file_elmts=1; - file_off=file_space->select.sel_info.pnt_lst->head->pnt[u] - +file_space->select.offset[u]; - break; - - default: - assert(0 && "Invalid selection type!"); - } /* end switch */ - - mem_size[u]=mem_space->extent.u.simple.size[u]; - size[u] = file_elmts; - file_offset[u] = file_off; - mem_offset[u] = mem_off; - } - mem_size[u]=elmt_size; - size[u] = elmt_size; - file_offset[u] = 0; - mem_offset[u] = 0; - - /* Write data to the file */ - if (H5F_arr_write(f, dxpl_id, layout, dc_plist, size, - mem_size, mem_offset, file_offset, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write data to the file"); - -done: - FUNC_LEAVE(ret_value); -} /* end H5S_all_write() */ - - /*-------------------------------------------------------------------------- NAME H5S_all_release @@ -925,147 +360,81 @@ done: /*-------------------------------------------------------------------------- NAME - H5S_all_select_iterate + H5S_all_select_get_seq_list PURPOSE - Iterate over a "all" selection, calling a user's function for each - element. + Create a list of offsets & lengths for a selection USAGE - herr_t H5S_all_select_iterate(buf, type_id, space, op, operator_data) - void *buf; IN/OUT: Buffer containing elements to iterate over - hid_t type_id; IN: Datatype ID of BUF array. - H5S_t *space; IN: Dataspace object containing selection to iterate over - H5D_operator_t op; IN: Function pointer to the routine to be - called for each element in BUF iterated over. - void *operator_data; IN/OUT: Pointer to any user-defined data - associated with the operation. + herr_t H5S_all_select_get_seq_list(flags,space,iter,elem_size,maxseq,maxbytes,nseq,nbytes,off,len) + unsigned flags; IN: Flags for extra information about operation + H5S_t *space; IN: Dataspace containing selection to use. + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + size_t elem_size; IN: Size of an element + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxbytes; IN: Maximum number of bytes to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + size_t *nbytes; OUT: Actual number of bytes in sequences generated + hsize_t *off; OUT: Array of offsets + size_t *len; OUT: Array of lengths RETURNS - Returns the return value of the last operator if it was non-zero, or zero - if all elements were processed. Otherwise returns a negative value. + Non-negative on success/Negative on failure. DESCRIPTION - Iterates over the selected elements in a memory buffer, calling the user's - callback function for each element. The selection in the dataspace is - modified so that any elements already iterated over are removed from the - selection if the iteration is interrupted (by the H5D_operator_t function - returning non-zero) in the "middle" of the iteration and may be re-started - by the user where it left off. - - NOTE: Until "subtracting" elements from a selection is implemented, - the selection is not modified. + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ herr_t -H5S_all_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op, - void *operator_data) +H5S_all_select_get_seq_list(unsigned UNUSED flags, const H5S_t *space,H5S_sel_iter_t *iter, + size_t elem_size, size_t maxseq, size_t maxbytes, size_t *nseq, size_t *nbytes, + hsize_t *off, size_t *len) { - hsize_t mem_size[H5O_LAYOUT_NDIMS]; /* Dataspace size */ - hsize_t mem_offset[H5O_LAYOUT_NDIMS]; /* current coordinates */ - hsize_t offset; /* offset of region in buffer */ - hsize_t nelemts; /* Number of elements to iterate through */ - void *tmp_buf; /* temporary location of the element in the buffer */ - unsigned rank; /* Dataspace rank */ - int indx; /* Index to increment */ - H5T_t *dt; /* Datatype structure */ - herr_t ret_value=0; /* return value */ + hsize_t bytes_left; /* The number of bytes left in the selection */ + hsize_t elem_used; /* The number of bytes used */ + herr_t ret_value=SUCCEED; /* return value */ - FUNC_ENTER_NOAPI(H5S_all_select_iterate, 0); + FUNC_ENTER_NOAPI (H5S_all_select_get_seq_list, FAIL); - assert(buf); + /* Check args */ assert(space); - assert(op); - assert(H5I_DATATYPE == H5I_get_type(type_id)); + assert(iter); + assert(elem_size>0); + assert(maxseq>0); + assert(maxbytes>0); + assert(nseq); + assert(nbytes); + assert(off); + assert(len); - /* Get the dataspace extent rank */ - rank=space->extent.u.simple.rank; - - /* Set up the size of the memory space */ - HDmemcpy(mem_size, space->extent.u.simple.size, rank*sizeof(hsize_t)); - - /* Set the size of the datatype */ - if (NULL==(dt=H5I_object(type_id))) - HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype"); - mem_size[rank]=H5T_get_size(dt); + /* Calculate the number of bytes left in the selection */ + bytes_left=iter->all.elmt_left*elem_size; - /* Set the coordinates to zero */ - HDmemset(mem_offset, 0, (rank+1)*sizeof(hsize_t)); + /* "round" off the maxbytes allowed to a multiple of the element size */ + maxbytes=(maxbytes/elem_size)*elem_size; - /* Get the number of elements to iterate through */ - nelemts=H5S_get_simple_extent_npoints(space); + /* Compute the offset in the dataset */ + off[0]=iter->all.offset*elem_size; + len[0]=MIN(maxbytes,bytes_left); - /* Iterate through the entire dataset */ - while(nelemts>0 && ret_value==0) { - /* Get the offset in the memory buffer */ - offset=H5V_array_offset(rank+1,mem_size,(const hssize_t *)mem_offset); - tmp_buf=((char *)buf+offset); + /* Should only need one sequence for 'all' selections */ + *nseq=1; - ret_value=(*op)(tmp_buf,type_id,(hsize_t)rank,(hssize_t *)mem_offset,operator_data); + /* Set the number of bytes used */ + *nbytes=len[0]; - /* Decrement the number of elements to iterate through */ - nelemts--; - - /* Advance the coordinate (currently in C memory order) */ - indx=rank-1; /* Leave the byte offset in the element alone */ - while(indx>=0 && ++mem_offset[indx]==mem_size[indx]) { - mem_offset[indx]=0; - indx--; - } /* end while */ - } /* end while */ - - FUNC_LEAVE (ret_value); -} /* H5S_all_select_iterate() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S_all_select_fill - PURPOSE - Fill an "all" selection in memory with a value - USAGE - herr_t H5S_all_select_fill(fill,fill_size,space,buf) - const void *fill; IN: Pointer to fill value to use - size_t fill_size; IN: Size of elements in memory buffer & size of - fill value - H5S_t *space; IN: Dataspace describing memory buffer & - containing selection to use. - void *buf; IN/OUT: Memory buffer to fill selection in - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to fill elements in a memory buffer. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - The memory buffer elements are assumed to have the same datatype as the - fill value being placed into them. - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -herr_t -H5S_all_select_fill(const void *fill, size_t fill_size, const H5S_t *space, void *buf) -{ - hssize_t nelemts; /* Number of elements in dataspace */ - herr_t ret_value=SUCCEED; /* return value */ - - FUNC_ENTER_NOAPI(H5S_all_select_fill, FAIL); - - /* Check args */ - assert(fill); - assert(fill_size>0); - assert(space); - assert(buf); - - /* Fill the selection in the memory buffer */ - - /* Get the number of elements to iterate through */ - if((nelemts=H5S_get_simple_extent_npoints(space))<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements"); - - /* Fill the elements in the buffer */ - H5_CHECK_OVERFLOW(nelemts,hssize_t,size_t); - H5V_array_fill(buf, fill, fill_size, (size_t)nelemts); + /* Update the iterator */ + elem_used=len[0]/elem_size; + iter->all.elmt_left-=elem_used; + iter->all.offset+=elem_used; +#ifdef LATER done: +#endif /* LATER */ FUNC_LEAVE (ret_value); -} /* H5S_all_select_fill() */ - +} /* end H5S_all_select_get_seq_list() */ diff --git a/src/H5Shyper.c b/src/H5Shyper.c index 0e30a73..04cecf6 100644 --- a/src/H5Shyper.c +++ b/src/H5Shyper.c @@ -10,17 +10,12 @@ #define H5S_PACKAGE /*suppress error about including H5Spkg */ -#include "H5private.h" -#include "H5Dprivate.h" -#include "H5Eprivate.h" -#include "H5Fprivate.h" -#include "H5FLprivate.h" /*Free Lists */ -#include "H5Iprivate.h" -#include "H5MMprivate.h" -#include "H5Pprivate.h" /* Property Lists */ -#include "H5Spkg.h" -#include "H5Tprivate.h" /* Datatypes */ -#include "H5Vprivate.h" +#include "H5private.h" /* Generic Functions */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5FLprivate.h" /* Free Lists */ +#include "H5Iprivate.h" /* ID Functions */ +#include "H5Spkg.h" /* Dataspace functions */ +#include "H5Vprivate.h" /* Vector functions */ /* Interface initialization */ #define PABLO_MASK H5Shyper_mask @@ -28,58 +23,14 @@ static int interface_initialize_g = 0; /* Local datatypes */ -/* Parameter block for H5S_hyper_select_iter_mem */ -typedef struct { - hid_t dt; - size_t elem_size; - const H5S_t *space; - H5S_sel_iter_t *iter; - void *src; - H5D_operator_t op; - void * op_data; -} H5S_hyper_iter_info_t; /* Static function prototypes */ -static herr_t H5S_hyper_init (const H5S_t *space, size_t elmt_size, H5S_sel_iter_t *iter); -static hsize_t H5S_hyper_favail (const H5S_t UNUSED *space, - const H5S_sel_iter_t *sel_iter, hsize_t max); -static hsize_t H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, H5S_sel_iter_t *file_iter, - hsize_t nelmts, hid_t dxpl_id, void *_buf/*out*/); -static herr_t H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, H5S_sel_iter_t *file_iter, - hsize_t nelmts, hid_t dxpl_id, const void *_buf); -static hsize_t H5S_hyper_mgath (const void *_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *_tconv_buf/*out*/); -static herr_t H5S_hyper_mscat (const void *_tconv_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *_buf/*out*/); static herr_t H5S_hyper_free_span_info (H5S_hyper_span_info_t *span_info); static herr_t H5S_hyper_free_span (H5S_hyper_span_t *span); static H5S_hyper_span_info_t *H5S_hyper_copy_span (H5S_hyper_span_info_t *spans); static herr_t H5S_hyper_span_scratch (H5S_hyper_span_info_t *spans, void *scr_value); static herr_t H5S_hyper_span_precompute (H5S_hyper_span_info_t *spans, size_t elmt_size); -const H5S_fconv_t H5S_HYPER_FCONV[1] = {{ - "hslab", /*name */ - H5S_SEL_HYPERSLABS, /*selection type */ - H5S_hyper_init, /*initialize */ - H5S_hyper_favail, /*available */ - H5S_hyper_fgath, /*gather */ - H5S_hyper_fscat, /*scatter */ -}}; - -const H5S_mconv_t H5S_HYPER_MCONV[1] = {{ - "hslab", /*name */ - H5S_SEL_HYPERSLABS, /*selection type */ - H5S_hyper_init, /*initialize */ - H5S_hyper_mgath, /*gather */ - H5S_hyper_mscat, /*scatter */ -}}; - /* Declare a free list to manage the H5S_hyper_span_t struct */ H5FL_DEFINE_STATIC(H5S_hyper_span_t); @@ -89,8 +40,8 @@ H5FL_ARR_DEFINE_STATIC(H5S_hyper_span_t,H5S_MAX_RANK); /* Declare a free list to manage the H5S_hyper_span_info_t struct */ H5FL_DEFINE_STATIC(H5S_hyper_span_info_t); -/* Declare a free list to manage arrays of size_t */ -H5FL_ARR_DEFINE_STATIC(size_t,-1); +/* Declare external the free list for hssize_t arrays */ +H5FL_ARR_EXTERN(hssize_t); /* Declare a free list to manage arrays of hsize_t */ H5FL_ARR_DEFINE_STATIC(hsize_t,-1); @@ -148,11 +99,14 @@ H5S_hyper_print_spans(const struct H5S_hyper_span_info_t *span_lst) * *------------------------------------------------------------------------- */ -static herr_t +herr_t H5S_hyper_init (const H5S_t *space, size_t elmt_size, H5S_sel_iter_t *sel_iter) { + unsigned cont_dim; /* Maximum contiguous dimension */ + const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ H5S_hyper_span_info_t *spans; /* Pointer to hyperslab span info node */ - unsigned u; /* Index variable */ + unsigned u; /* Index variable */ + int i; /* Index variable */ FUNC_ENTER_NOAPI(H5S_hyper_init, FAIL); @@ -163,14 +117,87 @@ H5S_hyper_init (const H5S_t *space, size_t elmt_size, H5S_sel_iter_t *sel_iter) /* Initialize the number of points to iterate over */ sel_iter->hyp.elmt_left=space->select.num_elem; + sel_iter->hyp.iter_rank=0; + + /* Set the temporary pointer to the dimension information */ + tdiminfo=space->select.sel_info.hslab.diminfo; /* Check for the special case of just one H5Sselect_hyperslab call made */ - if(space->select.sel_info.hslab.diminfo!=NULL) { + if(tdiminfo!=NULL) { /* Initialize the information needed for regular hyperslab I/O */ - /* Allocate the position & initialize to initial location */ - sel_iter->hyp.off = H5FL_ARR_ALLOC(hsize_t,space->extent.u.simple.rank,0); - for(u=0; u<space->extent.u.simple.rank; u++) - sel_iter->hyp.off[u]=space->select.sel_info.hslab.diminfo[u].start; + const hsize_t *mem_size; /* Temporary pointer to dataspace extent's dimension sizes */ + hsize_t acc; /* Accumulator for "flattened" dimension's sizes */ + + /* Set the temporary pointer to the dataspace extent's dimension sizes */ + mem_size=space->extent.u.simple.size; + + /* + * For a regular hyperslab to be contiguous up to some dimension, it + * must have only one block (i.e. count==1 in all dimensions up to that + * dimension) and the block size must be the same as the dataspace's + * extent in that dimension and all dimensions up to that dimension. + */ + + /* Initialize the number of contiguous dimensions to be the same as the dataspace's rank */ + cont_dim=space->extent.u.simple.rank; + + /* Check for a "contiguous" block */ + for(u=space->extent.u.simple.rank-1; u>0; u--) { + if(tdiminfo[u].count==1 && tdiminfo[u].block==mem_size[u]) + cont_dim=u; + } /* end for */ + + /* Check if the regular selection can be "flattened" */ + if(cont_dim<space->extent.u.simple.rank) { + /* Set the iterator's rank to the contiguous dimensions */ + sel_iter->hyp.iter_rank=cont_dim; + + /* Allocate the position & initialize to initial location */ + sel_iter->hyp.off = H5FL_ARR_ALLOC(hsize_t,cont_dim,0); + sel_iter->hyp.diminfo = H5FL_ARR_ALLOC(H5S_hyper_dim_t,cont_dim,0); + sel_iter->hyp.size = H5FL_ARR_ALLOC(hsize_t,cont_dim,0); + sel_iter->hyp.sel_off = H5FL_ARR_ALLOC(hssize_t,cont_dim,0); + + /* "Flatten" dataspace extent and selection information */ + for(i=space->extent.u.simple.rank-1, acc=1; i>=0; i--) { + if(tdiminfo[i].block==mem_size[i] && i>0) { + assert(tdiminfo[i].start==0); + acc *= mem_size[i]; + } /* end if */ + else { + if((unsigned)i==(cont_dim-1)) { + sel_iter->hyp.diminfo[i].start = tdiminfo[i].start*acc; + /* Special case for stride==1 regular selections */ + if(tdiminfo[i].stride==1) + sel_iter->hyp.diminfo[i].stride = 1; + else + sel_iter->hyp.diminfo[i].stride = tdiminfo[i].stride*acc; + sel_iter->hyp.diminfo[i].count = tdiminfo[i].count; + sel_iter->hyp.diminfo[i].block = tdiminfo[i].block*acc; + sel_iter->hyp.size[i] = mem_size[i]*acc; + sel_iter->hyp.sel_off[i] = space->select.offset[i]*acc; + } /* end if */ + else { + sel_iter->hyp.diminfo[i].start = tdiminfo[i].start; + sel_iter->hyp.diminfo[i].stride = tdiminfo[i].stride; + sel_iter->hyp.diminfo[i].count = tdiminfo[i].count; + sel_iter->hyp.diminfo[i].block = tdiminfo[i].block; + sel_iter->hyp.size[i] = mem_size[i]; + sel_iter->hyp.sel_off[i] = space->select.offset[i]; + } /* end else */ + } /* end if */ + } /* end for */ + + /* Initialize "flattened" iterator offset to initial location and dataspace extent and selection information to correct values */ + for(u=0; u<cont_dim; u++) + sel_iter->hyp.off[u]=sel_iter->hyp.diminfo[u].start; + } /* end if */ + else { + /* Allocate the position & initialize to initial location */ + sel_iter->hyp.off = H5FL_ARR_ALLOC(hsize_t,space->extent.u.simple.rank,0); + for(u=0; u<space->extent.u.simple.rank; u++) + sel_iter->hyp.off[u]=tdiminfo[u].start; + } /* end else */ } /* end if */ else { /* Initialize the information needed for non-regular hyperslab I/O */ @@ -231,10 +258,23 @@ H5S_hyper_sel_iter_release (H5S_sel_iter_t *sel_iter) /* Check args */ assert (sel_iter); - /* Release the array of offsets/positions */ + /* Release the common array of offsets/positions */ if(sel_iter->hyp.off!=NULL) H5FL_ARR_FREE(hsize_t,sel_iter->hyp.off); +/* Release the information needed for "flattened" regular hyperslab I/O */ + /* Free the "flattened" dataspace extent */ + if(sel_iter->hyp.size!=NULL) + H5FL_ARR_FREE(hsize_t,sel_iter->hyp.size); + + /* Free the "flattened" regular hyperslab selection */ + if(sel_iter->hyp.diminfo!=NULL) + H5FL_ARR_FREE(H5S_hyper_dim_t,sel_iter->hyp.diminfo); + + /* Free the "flattened" selection offset */ + if(sel_iter->hyp.sel_off!=NULL) + H5FL_ARR_FREE(hssize_t,sel_iter->hyp.sel_off); + /* Release the information needed for non-regular hyperslab I/O */ /* Free the copy of the selections span tree */ if(sel_iter->hyp.spans!=NULL) @@ -262,7 +302,7 @@ H5S_hyper_sel_iter_release (H5S_sel_iter_t *sel_iter) * *------------------------------------------------------------------------- */ -static hsize_t +hsize_t H5S_hyper_favail (const H5S_t * UNUSED space, const H5S_sel_iter_t *sel_iter, hsize_t max) { @@ -296,8 +336,9 @@ H5S_hyper_favail (const H5S_t * UNUSED space, *------------------------------------------------------------------------- */ static int -H5S_hyper_iter_next (const H5S_t *file_space, H5S_sel_iter_t *file_iter) +H5S_hyper_iter_next (const H5S_t *space, H5S_sel_iter_t *iter) { + const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ hsize_t iter_offset[H5O_LAYOUT_NDIMS]; hsize_t iter_count[H5O_LAYOUT_NDIMS]; int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ @@ -307,19 +348,33 @@ H5S_hyper_iter_next (const H5S_t *file_space, H5S_sel_iter_t *file_iter) FUNC_ENTER_NOINIT(H5S_hyper_iter_next); - /* Set some useful rank information */ - fast_dim=file_space->extent.u.simple.rank-1; - ndims=file_space->extent.u.simple.rank; + /* Check if this is a "flattened" regular hyperslab selection */ + if(iter->hyp.iter_rank!=0 && iter->hyp.iter_rank<space->extent.u.simple.rank) { + /* Set the aliases for a few important dimension ranks */ + ndims=iter->hyp.iter_rank; + fast_dim=ndims-1; + + /* Set the local copy of the diminfo pointer */ + tdiminfo=iter->hyp.diminfo; + } /* end if */ + else { + /* Set the aliases for a few important dimension ranks */ + ndims=space->extent.u.simple.rank; + fast_dim=ndims-1; + + /* Set the local copy of the diminfo pointer */ + tdiminfo=space->select.sel_info.hslab.diminfo; + } /* end else */ /* Calculate the offset and block count for each dimension */ for(i=0; i<ndims; i++) { - if(file_space->select.sel_info.hslab.diminfo[i].stride==1) { - iter_offset[i]=file_iter->hyp.off[i]-file_space->select.sel_info.hslab.diminfo[i].start; + if(tdiminfo[i].stride==1) { + iter_offset[i]=iter->hyp.off[i]-tdiminfo[i].start; iter_count[i]=0; } /* end if */ else { - iter_offset[i]=(file_iter->hyp.off[i]-file_space->select.sel_info.hslab.diminfo[i].start)%file_space->select.sel_info.hslab.diminfo[i].stride; - iter_count[i]=(file_iter->hyp.off[i]-file_space->select.sel_info.hslab.diminfo[i].start)/file_space->select.sel_info.hslab.diminfo[i].stride; + iter_offset[i]=(iter->hyp.off[i]-tdiminfo[i].start)%tdiminfo[i].stride; + iter_count[i]=(iter->hyp.off[i]-tdiminfo[i].start)/tdiminfo[i].stride; } /* end else */ } /* end for */ @@ -332,7 +387,7 @@ H5S_hyper_iter_next (const H5S_t *file_space, H5S_sel_iter_t *file_iter) iter_count[temp_dim]++; /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(iter_count[temp_dim]<file_space->select.sel_info.hslab.diminfo[temp_dim].count) + if(iter_count[temp_dim]<tdiminfo[temp_dim].count) break; else iter_count[temp_dim]=0; /* reset back to the beginning of the line */ @@ -342,7 +397,7 @@ H5S_hyper_iter_next (const H5S_t *file_space, H5S_sel_iter_t *file_iter) iter_offset[temp_dim]++; /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(iter_offset[temp_dim]<file_space->select.sel_info.hslab.diminfo[temp_dim].block) + if(iter_offset[temp_dim]<tdiminfo[temp_dim].block) break; else { /* Move to the next block in the current dimension */ @@ -350,7 +405,7 @@ H5S_hyper_iter_next (const H5S_t *file_space, H5S_sel_iter_t *file_iter) iter_count[temp_dim]++; /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(iter_count[temp_dim]<file_space->select.sel_info.hslab.diminfo[temp_dim].count) + if(iter_count[temp_dim]<tdiminfo[temp_dim].count) break; else iter_count[temp_dim]=0; /* reset back to the beginning of the line */ @@ -363,3735 +418,12 @@ H5S_hyper_iter_next (const H5S_t *file_space, H5S_sel_iter_t *file_iter) /* Translate current iter_offset and iter_count into iterator position */ for(i=0; i<ndims; i++) - file_iter->hyp.off[i]=file_space->select.sel_info.hslab.diminfo[i].start+(file_space->select.sel_info.hslab.diminfo[i].stride*iter_count[i])+iter_offset[i]; + iter->hyp.off[i]=tdiminfo[i].start+(tdiminfo[i].stride*iter_count[i])+iter_offset[i]; FUNC_LEAVE (SUCCEED); } /* H5S_hyper_iter_next() */ -/*------------------------------------------------------------------------- - * Function: H5S_hyper_fread - * - * Purpose: Performs an optimized gather from the file, based on a hyperslab - * span tree. - * - * Return: Success: Number of elements copied. - * Failure: 0 - * - * Programmer: Quincey Koziol - * Friday, September 8, 2000 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hsize_t -H5S_hyper_fread (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *space, H5S_sel_iter_t *iter, - hsize_t nelem, hid_t dxpl_id, void *_buf/*out*/) -{ - uint8_t *dst=(uint8_t *)_buf; /* Alias for pointer arithmetic */ - H5S_hyper_span_t **ispan; /* Iterator's hyperslab span nodes */ - H5S_hyper_span_t *curr_span; /* Current hyperslab span node */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Cumulative size of each dimension in bytes */ - hsize_t acc; /* Accumulator for computing cumulative sizes */ - hssize_t *abs_arr; /* Absolute hyperslab span position */ - hssize_t *off_arr; /* Offset within the dataspace extent */ - int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int curr_dim; /* Current dimension being operated on */ - int ndims; /* Number of dimensions of dataset */ - hsize_t loc_off; /* Element offset in the dataspace */ - size_t span_size=0; /* Number of bytes in current span to actually process */ - size_t io_bytes_left; /* Number of bytes left to process */ - int i; /* Index variable */ - size_t *seq_len_arr=NULL; /* Array of sequence lengths */ - hsize_t *buf_off_arr=NULL; /* Array of dataset offsets */ - size_t last_io_bytes_left=0; /* Last I/O bytes left before readv() called */ - size_t nseq=0; /* Number of sequence/offsets stored in the arrays */ - size_t vector_size; /* Value for vector size */ - H5P_genplist_t *plist; /* Property list */ - hssize_t ret_value=FAIL; - - FUNC_ENTER_NOINIT(H5S_hyper_fread); - - /* Check args */ - assert(f); - assert(layout); - assert(elmt_size>0); - assert(space); - assert(iter); - assert(nelem>0); - assert(dst); - - /* Set the rank of the fastest changing dimension */ - ndims=space->extent.u.simple.rank; - fast_dim=(ndims-1); - - /* Get the pointers to the current span info and span nodes */ - curr_span=iter->hyp.span[fast_dim]; - abs_arr=iter->hyp.off; - off_arr=space->select.offset; - ispan=iter->hyp.span; - - /* Set the amount of elements to perform I/O on, etc. */ - H5_ASSIGN_OVERFLOW(io_bytes_left,(nelem*elmt_size),hsize_t,size_t); - - /* Compute the cumulative size of dataspace dimensions */ - for(i=fast_dim, acc=elmt_size; i>=0; i--) { - slab[i]=acc; - acc*=space->extent.u.simple.size[i]; - } /* end for */ - - /* Set the offset of the first element iterated on */ - for(i=0, loc_off=0; i<ndims; i++) - /* Compute the sequential element offset */ - loc_off+=(abs_arr[i]+space->select.offset[i])*slab[i]; - - /* Get the hyperslab vector size */ - if(TRUE!=H5P_isa_class(dxpl_id,H5P_DATASET_XFER) || NULL == (plist = H5I_object(dxpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file access property list"); - if (H5P_get(plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, 0, "unable to get value"); - - /* Allocate the vector I/O arrays */ - if((seq_len_arr = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate vector I/O array"); - if((buf_off_arr = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate vector I/O array"); - - /* Range check against number of elements left in selection */ - assert(io_bytes_left<=(iter->hyp.elmt_left*elmt_size)); - - /* Take care of any partial spans leftover from previous I/Os */ - if(abs_arr[fast_dim]!=curr_span->low) { - - /* Finish the span in the fastest changing dimension */ - - /* Compute the number of bytes to attempt in this span */ - H5_ASSIGN_OVERFLOW(span_size,((curr_span->high-abs_arr[fast_dim])+1)*elmt_size,hsize_t,size_t); - - /* Check number of bytes against upper bounds allowed */ - if(span_size>io_bytes_left) - span_size=io_bytes_left; - - if (H5F_seq_read(f, dxpl_id, layout, dc_plist, space, - elmt_size, span_size, loc_off, dst/*out*/)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); - - /* Increment offset in destination */ - dst+=span_size; - - /* Decrement I/O left to perform */ - io_bytes_left-=span_size; - - /* Check if we are done */ - if(io_bytes_left>0) { - /* Move to next span in fastest changing dimension */ - curr_span=curr_span->next; - - if(curr_span!=NULL) { - /* Move location offset of destination */ - loc_off+=(curr_span->low-abs_arr[fast_dim])*elmt_size; - - /* Move iterator for fastest changing dimension */ - abs_arr[fast_dim]=curr_span->low; - } /* end if */ - } /* end if */ - else { - abs_arr[fast_dim]+=span_size/elmt_size; - - /* Check if we are still within the span */ - if(abs_arr[fast_dim]<=curr_span->high) { - iter->hyp.span[fast_dim]=curr_span; - - goto partial_done; /* finished with partial span */ - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[fast_dim]=curr_span->low; - iter->hyp.span[fast_dim]=curr_span; - - goto partial_done; /* finished with partial span */ - } /* end if */ - } /* end else */ - } /* end else */ - - /* Adjust iterator pointers */ - - if(curr_span==NULL) { -/* Same as code in main loop */ - /* Start at the next fastest dim */ - curr_dim=fast_dim-1; - - /* Work back up through the dimensions */ - while(curr_dim>=0) { - /* Reset the current span */ - curr_span=iter->hyp.span[curr_dim]; - - /* Increment absolute position */ - abs_arr[curr_dim]++; - - /* Check if we are still within the span */ - if(abs_arr[curr_dim]<=curr_span->high) { - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[curr_dim]=curr_span->low; - - break; - } /* end if */ - else { - /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ - curr_dim--; - } /* end else */ - } /* end else */ - } /* end while */ - - /* Check if we are finished with the spans in the tree */ - if(curr_dim<0) { - /* We had better be done with I/O or bad things are going to happen... */ - assert(io_bytes_left==0); - - goto partial_done; /* finished with partial span */ - } /* end if */ - else { - /* Reset the span in the current dimension */ - ispan[curr_dim]=curr_span; - - /* Walk back down the iterator positions, reseting them */ - while(curr_dim<fast_dim) { - assert(curr_span); - assert(curr_span->down); - assert(curr_span->down->head); - - /* Set the new span_info & span for this dimension */ - iter->hyp.span[curr_dim+1]=curr_span->down->head; - - /* Advance span down the tree */ - curr_span=curr_span->down->head; - - /* Reset the absolute offset for the dim */ - abs_arr[curr_dim+1]=curr_span->low; - - /* Increment current dimension */ - curr_dim++; - } /* end while */ - - /* Verify that the curr_span points to the fastest dim */ - assert(curr_span==iter->hyp.span[fast_dim]); - } /* end else */ - - /* Reset the buffer offset */ - for(i=0, loc_off=0; i<ndims; i++) - loc_off+=(abs_arr[i]+off_arr[i])*slab[i]; - } /* end if */ - } /* end if */ - -partial_done: /* Yes, goto's are evil, so sue me... :-) */ - /* Get the number of bytes left to process currently */ - last_io_bytes_left=io_bytes_left; - - /* Perform the I/O on the elements, based on the position of the iterator */ - while(io_bytes_left>0) { - /* Adjust location offset of destination to compensate for initial increment below */ - loc_off-=curr_span->pstride; - - /* Loop over all the spans in the fastest changing dimension */ - while(curr_span!=NULL) { - /* Move location offset of destination */ - loc_off+=curr_span->pstride; - - /* Compute the number of elements to attempt in this span */ - H5_ASSIGN_OVERFLOW(span_size,curr_span->nelem,hsize_t,size_t); - - /* Check number of elements against upper bounds allowed */ - if(span_size>=io_bytes_left) { - /* Trim the number of bytes to output */ - span_size=io_bytes_left; - io_bytes_left=0; - -/* COMMON */ - /* Store the I/O information for the span */ - seq_len_arr[nseq]=span_size; - buf_off_arr[nseq]=loc_off; - - /* Increment the number of sequences in arrays */ - nseq++; - - /* If the sequence & offset arrays are full, read them in */ - if(nseq>=vector_size) { - /* Read in the sequences */ - if (H5F_seq_readv(f, dxpl_id, layout, dc_plist, space, - elmt_size, nseq, seq_len_arr, buf_off_arr, dst/*out*/)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); - - /* Increment the offset of the destination buffer */ - dst+=(last_io_bytes_left-io_bytes_left); - - /* Keep around the current number of I/O bytes left */ - last_io_bytes_left=io_bytes_left; - nseq=0; - } /* end else */ -/* end COMMON */ - - /* Break out now, we are finished with I/O */ - break; - } /* end if */ - else { - /* Decrement I/O left to perform */ - io_bytes_left-=span_size; - -/* COMMON */ - /* Store the I/O information for the span */ - seq_len_arr[nseq]=span_size; - buf_off_arr[nseq]=loc_off; - - /* Increment the number of sequences in arrays */ - nseq++; - - /* If the sequence & offset arrays are full, read them in */ - if(nseq>=vector_size) { - /* Read in the sequences */ - if (H5F_seq_readv(f, dxpl_id, layout, dc_plist, space, - elmt_size, nseq, seq_len_arr, buf_off_arr, dst/*out*/)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); - - /* Increment the offset of the destination buffer */ - dst+=(last_io_bytes_left-io_bytes_left); - - /* Keep around the current number of I/O bytes left */ - last_io_bytes_left=io_bytes_left; - nseq=0; - } /* end else */ -/* end COMMON */ - } /* end else */ - - /* Move to next span in fastest changing dimension */ - curr_span=curr_span->next; - } /* end while */ - - /* Check if we are done */ - if(io_bytes_left==0) { - abs_arr[fast_dim]=curr_span->low+(span_size/elmt_size); - - /* Check if we are still within the span */ - if(abs_arr[fast_dim]<=curr_span->high) { - iter->hyp.span[fast_dim]=curr_span; - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[fast_dim]=curr_span->low; - iter->hyp.span[fast_dim]=curr_span; - break; - } /* end if */ - } /* end else */ - } /* end if */ - - /* Adjust iterator pointers */ - - /* Start at the next fastest dim */ - curr_dim=fast_dim-1; - - /* Work back up through the dimensions */ - while(curr_dim>=0) { - /* Reset the current span */ - curr_span=iter->hyp.span[curr_dim]; - - /* Increment absolute position */ - abs_arr[curr_dim]++; - - /* Check if we are still within the span */ - if(abs_arr[curr_dim]<=curr_span->high) { - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[curr_dim]=curr_span->low; - - break; - } /* end if */ - else { - /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ - curr_dim--; - } /* end else */ - } /* end else */ - } /* end while */ - - /* Check if we are finished with the spans in the tree */ - if(curr_dim<0) { - /* We had better be done with I/O or bad things are going to happen... */ - assert(io_bytes_left==0); - break; - } /* end if */ - else { - /* Reset the span in the current dimension */ - ispan[curr_dim]=curr_span; - - /* Walk back down the iterator positions, reseting them */ - while(curr_dim<fast_dim) { - assert(curr_span); - assert(curr_span->down); - assert(curr_span->down->head); - - /* Set the new span for the next dimension down */ - iter->hyp.span[curr_dim+1]=curr_span->down->head; - - /* Advance span down the tree */ - curr_span=curr_span->down->head; - - /* Reset the absolute offset for the dim */ - abs_arr[curr_dim+1]=curr_span->low; - - /* Increment current dimension */ - curr_dim++; - } /* end while */ - - /* Verify that the curr_span points to the fastest dim */ - assert(curr_span==iter->hyp.span[fast_dim]); - } /* end else */ - - /* Reset the buffer offset */ - for(i=0, loc_off=0; i<ndims; i++) - loc_off+=(abs_arr[i]+off_arr[i])*slab[i]; - } /* end while */ - - /* Check for any stored sequences which need to be flushed */ - if(nseq>0) { - /* Read in the sequence */ - if (H5F_seq_readv(f, dxpl_id, layout, dc_plist, space, - elmt_size, nseq, seq_len_arr, buf_off_arr, dst/*out*/)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); - } /* end if */ - - /* Increment amount of I/O performed */ - iter->hyp.elmt_left-=nelem; - - /* Success! */ - ret_value=nelem; - -done: - if(seq_len_arr!=NULL) - H5FL_ARR_FREE(size_t,seq_len_arr); - if(buf_off_arr!=NULL) - H5FL_ARR_FREE(hsize_t,buf_off_arr); - - FUNC_LEAVE (ret_value); -} /* H5S_hyper_fread() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_hyper_fread_opt - * - * Purpose: Performs an optimized gather from the file, based on a regular - * hyperslab (i.e. one which was generated from just one call to - * H5Sselect_hyperslab). - * - * Return: Success: Number of elements copied. - * Failure: 0 - * - * Programmer: Quincey Koziol - * Friday, September 8, 2000 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hsize_t -H5S_hyper_fread_opt (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, H5S_sel_iter_t *file_iter, - hsize_t nelmts, hid_t dxpl_id, void *_buf/*out*/) -{ - size_t *seq_len_arr=NULL; /* Array of sequence lengths */ - hsize_t *buf_off_arr=NULL; /* Array of dataset offsets */ - size_t nseq=0; /* Number of sequence/offsets stored in the arrays */ - size_t tot_buf_size=0; /* Total number of bytes in buffer */ - - hssize_t offset[H5O_LAYOUT_NDIMS]; /* Offset on disk */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */ - hssize_t wrap[H5O_LAYOUT_NDIMS]; /* Bytes to wrap around at the end of a row */ - hsize_t skip[H5O_LAYOUT_NDIMS]; /* Bytes to skip between blocks */ - hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary block count */ - hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary block offset */ - uint8_t *buf=(uint8_t *)_buf; /* Alias for pointer arithmetic */ - const H5S_hyper_dim_t *tdiminfo; /* Local pointer to diminfo information */ - hssize_t fast_dim_start, /* Local copies of fastest changing dimension info */ - fast_dim_offset; - hsize_t fast_dim_stride, /* Local copies of fastest changing dimension info */ - fast_dim_block, - fast_dim_buf_off; - size_t fast_dim_count; - size_t tot_blk_count; /* Total number of blocks left to output */ - size_t act_blk_count; /* Actual number of blocks to output */ - int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int temp_dim; /* Temporary rank holder */ - hsize_t acc; /* Accumulator */ - hsize_t buf_off; /* Current buffer offset for copying memory */ - int i; /* Counters */ - unsigned u; /* Counters */ - int ndims; /* Number of dimensions of dataset */ - size_t actual_read; /* The actual number of elements to read in */ - size_t actual_bytes; /* The actual number of bytes to copy */ - size_t io_left; /* The number of elements left in I/O operation */ - size_t tot_seq; /* The number of sequences filled */ - hsize_t *buf_off_arr_p; /* Pointer into the buffer offset array */ - size_t seq_count; /* Temporary count of sequences left to process */ -#ifndef NO_DUFFS_DEVICE - size_t duffs_index; /* Counting index for Duff's device */ -#endif /* NO_DUFFS_DEVICE */ - size_t vector_size; /* Value for vector size */ - H5P_genplist_t *plist; /* Property list */ - hsize_t ret_value=0; /* Return value */ - - FUNC_ENTER_NOINIT(H5S_hyper_fread_opt); - - /* Get the hyperslab vector size */ - if(TRUE!=H5P_isa_class(dxpl_id,H5P_DATASET_XFER) || NULL == (plist = H5I_object(dxpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a file access property list"); - if (H5P_get(plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, 0, "unable to get value"); - - /* Allocate the vector I/O arrays */ - if((seq_len_arr = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate vector I/O array"); - if((buf_off_arr = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate vector I/O array"); - - /* Set the rank of the fastest changing dimension */ - fast_dim=file_space->extent.u.simple.rank-1; - ndims=file_space->extent.u.simple.rank; - - /* initialize row sizes for each dimension */ - for(i=(ndims-1),acc=1; i>=0; i--) { - slab[i]=acc*elmt_size; - acc*=file_space->extent.u.simple.size[i]; - } /* end for */ - - /* Set the number of elements left for I/O */ - H5_ASSIGN_OVERFLOW(io_left,nelmts,hsize_t,size_t); - - /* Check if we stopped in the middle of a sequence of elements */ - if((file_iter->hyp.off[fast_dim]-file_space->select.sel_info.hslab.diminfo[fast_dim].start)%file_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0 || - ((file_iter->hyp.off[fast_dim]!=file_space->select.sel_info.hslab.diminfo[fast_dim].start) && file_space->select.sel_info.hslab.diminfo[fast_dim].stride==1)) { - hsize_t leftover; /* The number of elements left over from the last sequence */ - - /* Calculate the number of elements left in the sequence */ - if(file_space->select.sel_info.hslab.diminfo[fast_dim].stride==1) - leftover=file_space->select.sel_info.hslab.diminfo[fast_dim].block-(file_iter->hyp.off[fast_dim]-file_space->select.sel_info.hslab.diminfo[fast_dim].start); - else - leftover=file_space->select.sel_info.hslab.diminfo[fast_dim].block-((file_iter->hyp.off[fast_dim]-file_space->select.sel_info.hslab.diminfo[fast_dim].start)%file_space->select.sel_info.hslab.diminfo[fast_dim].stride); - - /* Make certain that we don't read too many */ - H5_CHECK_OVERFLOW(leftover,hsize_t,size_t); - actual_read=MIN((size_t)leftover,io_left); - actual_bytes=actual_read*elmt_size; - - /* Copy the location of the point to get */ - HDmemcpy(offset, file_iter->hyp.off,ndims*sizeof(hssize_t)); - offset[ndims] = 0; - - /* Add in the selection offset */ - for(i=0; i<ndims; i++) - offset[i] += file_space->select.offset[i]; - - /* Compute the initial buffer offset */ - for(i=0,buf_off=0; i<ndims; i++) - buf_off+=offset[i]*slab[i]; - - /* Read in the rest of the sequence */ - if (H5F_seq_read(f, dxpl_id, layout, dc_plist, file_space, - elmt_size, actual_bytes, buf_off, buf/*out*/)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); - - /* Increment the offset of the buffer */ - buf+=actual_bytes; - - /* Decrement the amount left to read */ - io_left-=actual_read; - - /* Advance the point iterator */ - /* If we had enough buffer space to read in the rest of the sequence - * in the fastest changing dimension, move the iterator offset to - * the beginning of the next block to read. Otherwise, just advance - * the iterator in the fastest changing dimension. - */ - if(actual_read==leftover) { - /* Move iterator offset to beginning of next sequence in the fastest changing dimension */ - H5S_hyper_iter_next(file_space,file_iter); - } /* end if */ - else { - file_iter->hyp.off[fast_dim]+=actual_read; /* whole sequence not read in, just advance fastest dimension offset */ - } /* end if */ - } /* end if */ - - /* Now that we've cleared the "remainder" of the previous fastest dimension - * sequence, we must be at the beginning of a sequence, so use the fancy - * algorithm to compute the offsets and run through as many as possible, - * until the buffer fills up. - */ - if(io_left>0) { /* Just in case the "remainder" above filled the buffer */ - /* Compute the arrays to perform I/O on */ - /* Copy the location of the point to get */ - HDmemcpy(offset, file_iter->hyp.off,ndims*sizeof(hssize_t)); - offset[ndims] = 0; - - /* Add in the selection offset */ - for(i=0; i<ndims; i++) - offset[i] += file_space->select.offset[i]; - - /* Compute the current "counts" for this location */ - for(i=0; i<ndims; i++) { - if(file_space->select.sel_info.hslab.diminfo[i].stride==1) { - tmp_count[i] = 0; - tmp_block[i] = file_iter->hyp.off[i]-file_space->select.sel_info.hslab.diminfo[i].start; - } /* end if */ - else { - tmp_count[i] = (file_iter->hyp.off[i]-file_space->select.sel_info.hslab.diminfo[i].start)/file_space->select.sel_info.hslab.diminfo[i].stride; - tmp_block[i] = (file_iter->hyp.off[i]-file_space->select.sel_info.hslab.diminfo[i].start)%file_space->select.sel_info.hslab.diminfo[i].stride; - } /* end else */ - } /* end for */ - - /* Compute the initial buffer offset */ - for(i=0,buf_off=0; i<ndims; i++) - buf_off+=offset[i]*slab[i]; - - /* Set the number of elements to read each time */ - H5_ASSIGN_OVERFLOW(actual_read,file_space->select.sel_info.hslab.diminfo[fast_dim].block,hsize_t,size_t); - - /* Set the number of actual bytes */ - actual_bytes=actual_read*elmt_size; - - /* Set the local copy of the diminfo pointer */ - tdiminfo=file_space->select.sel_info.hslab.diminfo; - - /* Set local copies of information for the fastest changing dimension */ - fast_dim_start=tdiminfo[fast_dim].start; - fast_dim_stride=tdiminfo[fast_dim].stride; - fast_dim_block=tdiminfo[fast_dim].block; - fast_dim_buf_off=slab[fast_dim]*fast_dim_stride; - fast_dim_offset=fast_dim_start+file_space->select.offset[fast_dim]; - - /* Compute the number of blocks which would fit into the buffer */ - H5_ASSIGN_OVERFLOW(tot_blk_count,(io_left/fast_dim_block),hsize_t,size_t); - - /* Compute the amount to wrap at the end of each row */ - for(i=0; i<ndims; i++) - wrap[i]=(file_space->extent.u.simple.size[i]-(tdiminfo[i].stride*tdiminfo[i].count))*slab[i]; - - /* Compute the amount to skip between blocks */ - for(i=0; i<ndims; i++) - skip[i]=(tdiminfo[i].stride-tdiminfo[i].block)*slab[i]; - - /* Fill the sequence length array (since they will all be the same for optimized hyperslabs) */ - for(u=0; u<vector_size; u++) - seq_len_arr[u]=actual_bytes; - - /* Read in data until an entire sequence can't be read in any longer */ - while(io_left>0) { - /* Reset copy of number of blocks in fastest dimension */ - H5_ASSIGN_OVERFLOW(fast_dim_count,tdiminfo[fast_dim].count-tmp_count[fast_dim],hsize_t,size_t); - - /* Check if this entire row will fit into buffer */ - if(fast_dim_count<=tot_blk_count) { - - /* Entire row of blocks fits into buffer */ - act_blk_count=fast_dim_count; - - /* Loop over all the blocks in the fastest changing dimension */ - while(fast_dim_count>0) { - /* Gather the sequence */ - - /* Compute the number of sequences to fill */ - tot_seq=MIN(vector_size-nseq,fast_dim_count); - - /* Get a copy of the number of sequences to fill */ - seq_count=tot_seq; - - /* Set the pointer to the correct starting array element */ - buf_off_arr_p=&buf_off_arr[nseq]; - -#ifdef NO_DUFFS_DEVICE - /* Fill up the buffer, or finish up the blocks in this dimension */ - while(seq_count>0) { - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - seq_count--; - } /* end while */ -#else /* NO_DUFFS_DEVICE */ - duffs_index = (seq_count + 7) / 8; - switch (seq_count % 8) { - case 0: - do - { - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 7: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 6: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 5: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 4: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 3: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 2: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 1: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - } while (--duffs_index > 0); - } /* end switch */ -#endif /* NO_DUFFS_DEVICE */ - - /* Increment number of array elements used */ - nseq+=tot_seq; - - /* Increment the total number of bytes contained in arrays */ - tot_buf_size += tot_seq*actual_bytes; - - /* Decrement number of blocks left */ - fast_dim_count -= tot_seq; - - /* If the sequence & offset arrays are full, read them in */ - if(nseq>=vector_size) { - /* Read in the sequences */ - if (H5F_seq_readv(f, dxpl_id, layout, dc_plist, file_space, - elmt_size, nseq, seq_len_arr, buf_off_arr, buf/*out*/)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); - - /* Increment the offset of the destination buffer */ - buf+=tot_buf_size; - - /* Reset the number of bytes & sequences */ - tot_buf_size=0; - nseq=0; - } /* end else */ - } /* end while */ - - /* Decrement number of elements left */ - io_left -= actual_read*act_blk_count; - - /* Decrement number of blocks left */ - tot_blk_count -= act_blk_count; - - /* Increment information to reflect block just processed */ - offset[fast_dim]=fast_dim_offset; /* reset the offset in the fastest dimension */ - tmp_count[fast_dim]=0; - - /* Increment offset in destination buffer */ - buf_off += wrap[fast_dim]; - } /* end if */ - else { - - /* Entire row of blocks doesn't fit into buffer */ - act_blk_count=tot_blk_count; - - /* Reduce number of blocks to output */ - fast_dim_count=tot_blk_count; - - /* Loop over all the blocks in the fastest changing dimension */ - while(fast_dim_count>0) { - /* Gather the sequence */ - - /* Compute the number of sequences to fill */ - tot_seq=MIN(vector_size-nseq,fast_dim_count); - - /* Get a copy of the number of sequences to fill */ - seq_count=tot_seq; - - /* Set the pointer to the correct starting array element */ - buf_off_arr_p=&buf_off_arr[nseq]; - - /* Fill up the buffer, or finish up the blocks in this dimension */ - while(seq_count>0) { - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - seq_count--; - } /* end while */ - - /* Increment number of array elements used */ - nseq+=tot_seq; - - /* Increment the total number of bytes contained in arrays */ - tot_buf_size += tot_seq*actual_bytes; - - /* Decrement number of blocks left */ - fast_dim_count -= tot_seq; - - /* If the sequence & offset arrays are full, read them in */ - if(nseq>=vector_size) { - /* Read in the sequences */ - if (H5F_seq_readv(f, dxpl_id, layout, dc_plist, file_space, - elmt_size, nseq, seq_len_arr, buf_off_arr, buf/*out*/)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); - - /* Increment the offset of the destination buffer */ - buf+=tot_buf_size; - - /* Reset the number of bytes & sequences */ - tot_buf_size=0; - nseq=0; - } /* end else */ - } /* end while */ - - /* Decrement number of elements left */ - io_left -= actual_read*act_blk_count; - - /* Decrement number of blocks left */ - tot_blk_count -= act_blk_count; - - /* Increment information to reflect block just processed */ - offset[fast_dim]+=(fast_dim_stride*act_blk_count); /* reset the offset in the fastest dimension */ - tmp_count[fast_dim]+=act_blk_count; - - /* Handle any leftover, partial blocks in this row */ - if(io_left>0) { - actual_read=io_left; - actual_bytes=actual_read*elmt_size; - - /* Gather the sequence */ - - /* Store of length & offset */ - seq_len_arr[nseq]=actual_bytes; - buf_off_arr[nseq]=buf_off; - - /* Increment the total number of bytes contained in arrays */ - tot_buf_size += actual_bytes; - - /* Increment the number of sequences in arrays */ - nseq++; - - /* If the sequence & offset arrays are full, read them in */ - if(nseq>=vector_size) { - /* Read in the sequences */ - if (H5F_seq_readv(f, dxpl_id, layout, dc_plist, file_space, - elmt_size, nseq, seq_len_arr, buf_off_arr, buf/*out*/)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); - - /* Increment the offset of the destination buffer */ - buf+=tot_buf_size; - - /* Reset the number of bytes & sequences */ - tot_buf_size=0; - nseq=0; - } /* end else */ - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - /* Decrement the number of elements left */ - io_left -= actual_read; - - /* Increment buffer correctly */ - offset[fast_dim]+=actual_read; - } /* end if */ - - /* don't bother checking slower dimensions */ - assert(tot_blk_count==0); - assert(io_left==0); - break; - } /* end else */ - - /* Increment the offset and count for the other dimensions */ - temp_dim=fast_dim-1; - while(temp_dim>=0) { - /* Move to the next row in the curent dimension */ - offset[temp_dim]++; - tmp_block[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_block[temp_dim]<tdiminfo[temp_dim].block) - break; - else { - /* Move to the next block in the current dimension */ - offset[temp_dim]+=(tdiminfo[temp_dim].stride-tdiminfo[temp_dim].block); - buf_off += skip[temp_dim]; - tmp_block[temp_dim]=0; - tmp_count[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_count[temp_dim]<tdiminfo[temp_dim].count) - break; - else { - offset[temp_dim]=tdiminfo[temp_dim].start+file_space->select.offset[temp_dim]; - buf_off += wrap[temp_dim]; - tmp_count[temp_dim]=0; /* reset back to the beginning of the line */ - tmp_block[temp_dim]=0; - } /* end else */ - } /* end else */ - - /* Decrement dimension count */ - temp_dim--; - } /* end while */ - } /* end while */ - - /* Check for any stored sequences which need to be flushed */ - if(nseq>0) { - /* Read in the sequence */ - if (H5F_seq_readv(f, dxpl_id, layout, dc_plist, file_space, - elmt_size, nseq, seq_len_arr, buf_off_arr, buf/*out*/)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); - } /* end if */ - - /* Subtract out the selection offset */ - for(i=0; i<ndims; i++) - offset[i] -= file_space->select.offset[i]; - - /* Update the iterator with the location we stopped */ - HDmemcpy(file_iter->hyp.off, offset, ndims*sizeof(hssize_t)); - } /* end if */ - - /* Decrement the number of elements left in selection */ - file_iter->hyp.elmt_left -= (nelmts-io_left); - - /* Set the return value */ - ret_value= (nelmts-io_left); - -done: - if(seq_len_arr!=NULL) - H5FL_ARR_FREE(size_t,seq_len_arr); - if(buf_off_arr!=NULL) - H5FL_ARR_FREE(hsize_t,buf_off_arr); - - FUNC_LEAVE (ret_value); -} /* H5S_hyper_fread_opt() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_hyper_fgath - * - * Purpose: Gathers data points from file F and accumulates them in the - * type conversion buffer BUF. The LAYOUT argument describes - * how the data is stored on disk and EFL describes how the data - * is organized in external files. ELMT_SIZE is the size in - * bytes of a datum which this function treats as opaque. - * FILE_SPACE describes the data space of the dataset on disk - * and the elements that have been selected for reading (via - * hyperslab, etc). This function will copy at most NELMTS elements. - * - * Return: Success: Number of elements copied. - * - * Failure: 0 - * - * Programmer: Quincey Koziol - * Tuesday, June 16, 1998 - * - * Modifications: - * Robb Matzke, 1999-08-03 - * The data transfer properties are passed by ID since that's - * what the virtual file layer needs. - *------------------------------------------------------------------------- - */ -static hsize_t -H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, H5S_sel_iter_t *file_iter, - hsize_t nelmts, hid_t dxpl_id, void *_buf/*out*/) -{ - hsize_t num_read=0; /* number of elements read into buffer */ - herr_t ret_value=SUCCEED; - - FUNC_ENTER_NOAPI(H5S_hyper_fgath, 0); - - /* Check args */ - assert (f); - assert (layout); - assert (elmt_size>0); - assert (file_space); - assert (file_iter); - assert (nelmts>0); - assert (_buf); - - /* Check for the special case of just one H5Sselect_hyperslab call made */ - if(file_space->select.sel_info.hslab.diminfo!=NULL) { - /* Use optimized call to read in regular hyperslab */ - num_read=H5S_hyper_fread_opt(f,layout,dc_plist,elmt_size,file_space,file_iter,nelmts,dxpl_id,_buf); - } /* end if */ - else { - /* Perform generic hyperslab operation */ - num_read=H5S_hyper_fread(f,layout,dc_plist,elmt_size,file_space,file_iter,nelmts,dxpl_id,_buf); - } /* end else */ - - FUNC_LEAVE (ret_value==SUCCEED ? num_read : 0); -} /* H5S_hyper_fgath() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_hyper_fwrite - * - * Purpose: Performs an optimized scatter to the file, based on a hyperslab - * span selection. - * - * Return: Success: Number of elements copied. - * Failure: 0 - * - * Programmer: Quincey Koziol - * Tuesday, September 12, 2000 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hsize_t -H5S_hyper_fwrite (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *space, H5S_sel_iter_t *iter, - hsize_t nelem, hid_t dxpl_id, const void *_buf) -{ - const uint8_t *src=(const uint8_t *)_buf; /* Alias for pointer arithmetic */ - H5S_hyper_span_t **ispan; /* Iterator's hyperslab span nodes */ - H5S_hyper_span_t *curr_span; /* Current hyperslab span node */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Cumulative size of each dimension in bytes */ - hsize_t acc; /* Accumulator for computing cumulative sizes */ - hssize_t *abs_arr; /* Absolute hyperslab span position */ - hssize_t *off_arr; /* Offset within the dataspace extent */ - int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int curr_dim; /* Current dimension being operated on */ - int ndims; /* Number of dimensions of dataset */ - hsize_t loc_off; /* Element offset in the dataspace */ - size_t span_size=0; /* Number of bytes in current span to actually process */ - size_t io_bytes_left; /* Number of bytes left to process */ - int i; /* Index variable */ - size_t *seq_len_arr=NULL; /* Array of sequence lengths */ - hsize_t *buf_off_arr=NULL; /* Array of dataset offsets */ - size_t last_io_bytes_left=0; /* Last I/O bytes left before readv() called */ - size_t nseq=0; /* Number of sequence/offsets stored in the arrays */ - size_t vector_size; /* Value for vector size */ - H5P_genplist_t *plist; /* Property list */ - hssize_t ret_value=FAIL; - - FUNC_ENTER_NOINIT(H5S_hyper_fwrite); - - /* Check args */ - assert(f); - assert(layout); - assert(elmt_size>0); - assert(space); - assert(iter); - assert(nelem>0); - assert(src); - - /* Set the rank of the fastest changing dimension */ - ndims=space->extent.u.simple.rank; - fast_dim=(ndims-1); - - /* Get the pointers to the current span info and span nodes */ - curr_span=iter->hyp.span[fast_dim]; - abs_arr=iter->hyp.off; - off_arr=space->select.offset; - ispan=iter->hyp.span; - - /* Set the amount of elements to perform I/O on, etc. */ - H5_ASSIGN_OVERFLOW(io_bytes_left,(nelem*elmt_size),hsize_t,size_t); - - /* Compute the cumulative size of dataspace dimensions */ - for(i=fast_dim, acc=elmt_size; i>=0; i--) { - slab[i]=acc; - acc*=space->extent.u.simple.size[i]; - } /* end for */ - - /* Set the offset of the first element iterated on */ - for(i=0, loc_off=0; i<ndims; i++) - /* Compute the sequential element offset */ - loc_off+=(abs_arr[i]+space->select.offset[i])*slab[i]; - - /* Range check against number of elements left in selection */ - assert(io_bytes_left<=(iter->hyp.elmt_left*elmt_size)); - - /* Get the hyperslab vector size */ - if(TRUE!=H5P_isa_class(dxpl_id,H5P_DATASET_XFER) || NULL == (plist = H5I_object(dxpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a file access property list"); - if (H5P_get(plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, 0, "unable to get value"); - - /* Allocate the vector I/O arrays */ - if((seq_len_arr = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate vector I/O array"); - if((buf_off_arr = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate vector I/O array"); - - /* Take care of any partial spans leftover from previous I/Os */ - if(abs_arr[fast_dim]!=curr_span->low) { - - /* Finish the span in the fastest changing dimension */ - - /* Compute the number of bytes to attempt in this span */ - H5_ASSIGN_OVERFLOW(span_size,((curr_span->high-abs_arr[fast_dim])+1)*elmt_size,hsize_t,size_t); - - /* Check number of bytes against upper bounds allowed */ - if(span_size>io_bytes_left) - span_size=io_bytes_left; - - if (H5F_seq_write(f, dxpl_id, layout, dc_plist, space, - elmt_size, span_size, loc_off, src)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); - - /* Increment offset in destination */ - src+=span_size; - - /* Decrement I/O left to perform */ - io_bytes_left-=span_size; - - /* Check if we are done */ - if(io_bytes_left>0) { - /* Move to next span in fastest changing dimension */ - curr_span=curr_span->next; - - if(curr_span!=NULL) { - /* Move location offset of destination */ - loc_off+=(curr_span->low-abs_arr[fast_dim])*elmt_size; - - /* Move iterator for fastest changing dimension */ - abs_arr[fast_dim]=curr_span->low; - } /* end if */ - } /* end if */ - else { - abs_arr[fast_dim]+=span_size/elmt_size; - - /* Check if we are still within the span */ - if(abs_arr[fast_dim]<=curr_span->high) { - iter->hyp.span[fast_dim]=curr_span; - - goto partial_done; /* finished with partial span */ - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[fast_dim]=curr_span->low; - iter->hyp.span[fast_dim]=curr_span; - - goto partial_done; /* finished with partial span */ - } /* end if */ - } /* end else */ - } /* end else */ - - /* Adjust iterator pointers */ - - if(curr_span==NULL) { -/* Same as code in main loop */ - /* Start at the next fastest dim */ - curr_dim=fast_dim-1; - - /* Work back up through the dimensions */ - while(curr_dim>=0) { - /* Reset the current span */ - curr_span=iter->hyp.span[curr_dim]; - - /* Increment absolute position */ - abs_arr[curr_dim]++; - - /* Check if we are still within the span */ - if(abs_arr[curr_dim]<=curr_span->high) { - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[curr_dim]=curr_span->low; - - break; - } /* end if */ - else { - /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ - curr_dim--; - } /* end else */ - } /* end else */ - } /* end while */ - - /* Check if we are finished with the spans in the tree */ - if(curr_dim<0) { - /* We had better be done with I/O or bad things are going to happen... */ - assert(io_bytes_left==0); - - goto partial_done; /* finished with partial span */ - } /* end if */ - else { - /* Reset the span in the current dimension */ - ispan[curr_dim]=curr_span; - - /* Walk back down the iterator positions, reseting them */ - while(curr_dim<fast_dim) { - assert(curr_span); - assert(curr_span->down); - assert(curr_span->down->head); - - /* Set the new span for this dimension */ - iter->hyp.span[curr_dim+1]=curr_span->down->head; - - /* Advance span down the tree */ - curr_span=curr_span->down->head; - - /* Reset the absolute offset for the dim */ - abs_arr[curr_dim+1]=curr_span->low; - - /* Increment current dimension */ - curr_dim++; - } /* end while */ - - /* Verify that the curr_span points to the fastest dim */ - assert(curr_span==iter->hyp.span[fast_dim]); - } /* end else */ - - /* Reset the buffer offset */ - for(i=0, loc_off=0; i<ndims; i++) - loc_off+=(abs_arr[i]+off_arr[i])*slab[i]; - } /* end if */ - } /* end if */ - -partial_done: /* Yes, goto's are evil, so sue me... :-) */ - /* Get the number of bytes left to process currently */ - last_io_bytes_left=io_bytes_left; - - /* Perform the I/O on the elements, based on the position of the iterator */ - while(io_bytes_left>0) { - /* Adjust location offset of destination to compensate for initial increment below */ - loc_off-=curr_span->pstride; - - /* Loop over all the spans in the fastest changing dimension */ - while(curr_span!=NULL) { - /* Move location offset of destination */ - loc_off+=curr_span->pstride; - - /* Compute the number of elements to attempt in this span */ - H5_ASSIGN_OVERFLOW(span_size,curr_span->nelem,hsize_t,size_t); - - /* Check number of elements against upper bounds allowed */ - if(span_size>=io_bytes_left) { - /* Trim the number of bytes to output */ - span_size=io_bytes_left; - io_bytes_left=0; - -/* COMMON */ - /* Store the I/O information for the span */ - seq_len_arr[nseq]=span_size; - buf_off_arr[nseq]=loc_off; - - /* Increment the number of sequences in arrays */ - nseq++; - - /* If the sequence & offset arrays are full, read them in */ - if(nseq>=vector_size) { - /* Write out the sequences */ - if (H5F_seq_writev(f, dxpl_id, layout, dc_plist, space, - elmt_size, nseq, seq_len_arr, buf_off_arr, src)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); - - /* Increment the offset of the destination buffer */ - src+=(last_io_bytes_left-io_bytes_left); - - /* Keep around the current number of I/O bytes left */ - last_io_bytes_left=io_bytes_left; - nseq=0; - } /* end else */ -/* end COMMON */ - - /* Break out now, we are finished with I/O */ - break; - } /* end if */ - else { - /* Decrement I/O left to perform */ - io_bytes_left-=span_size; - -/* COMMON */ - /* Store the I/O information for the span */ - seq_len_arr[nseq]=span_size; - buf_off_arr[nseq]=loc_off; - - /* Increment the number of sequences in arrays */ - nseq++; - - /* If the sequence & offset arrays are full, read them in */ - if(nseq>=vector_size) { - /* Write out the sequences */ - if (H5F_seq_writev(f, dxpl_id, layout, dc_plist, space, - elmt_size, nseq, seq_len_arr, buf_off_arr, src)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); - - /* Increment the offset of the destination buffer */ - src+=(last_io_bytes_left-io_bytes_left); - - /* Keep around the current number of I/O bytes left */ - last_io_bytes_left=io_bytes_left; - nseq=0; - } /* end else */ -/* end COMMON */ - } /* end else */ - - /* Move to next span in fastest changing dimension */ - curr_span=curr_span->next; - } /* end while */ - - /* Check if we are done */ - if(io_bytes_left==0) { - abs_arr[fast_dim]=curr_span->low+(span_size/elmt_size); - - /* Check if we are still within the span */ - if(abs_arr[fast_dim]<=curr_span->high) { - iter->hyp.span[fast_dim]=curr_span; - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[fast_dim]=curr_span->low; - iter->hyp.span[fast_dim]=curr_span; - break; - } /* end if */ - } /* end else */ - } /* end if */ - - /* Adjust iterator pointers */ - - /* Start at the next fastest dim */ - curr_dim=fast_dim-1; - - /* Work back up through the dimensions */ - while(curr_dim>=0) { - /* Reset the current span */ - curr_span=iter->hyp.span[curr_dim]; - - /* Increment absolute position */ - abs_arr[curr_dim]++; - - /* Check if we are still within the span */ - if(abs_arr[curr_dim]<=curr_span->high) { - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[curr_dim]=curr_span->low; - - break; - } /* end if */ - else { - /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ - curr_dim--; - } /* end else */ - } /* end else */ - } /* end while */ - - /* Check if we are finished with the spans in the tree */ - if(curr_dim<0) { - /* We had better be done with I/O or bad things are going to happen... */ - assert(io_bytes_left==0); - break; - } /* end if */ - else { - /* Reset the span in the current dimension */ - ispan[curr_dim]=curr_span; - - /* Walk back down the iterator positions, reseting them */ - while(curr_dim<fast_dim) { - assert(curr_span); - assert(curr_span->down); - assert(curr_span->down->head); - - /* Set the new span for the next dimension down */ - iter->hyp.span[curr_dim+1]=curr_span->down->head; - - /* Advance span down the tree */ - curr_span=curr_span->down->head; - - /* Reset the absolute offset for the dim */ - abs_arr[curr_dim+1]=curr_span->low; - - /* Increment current dimension */ - curr_dim++; - } /* end while */ - - /* Verify that the curr_span points to the fastest dim */ - assert(curr_span==iter->hyp.span[fast_dim]); - } /* end else */ - - /* Reset the buffer offset */ - for(i=0, loc_off=0; i<ndims; i++) - loc_off+=(abs_arr[i]+off_arr[i])*slab[i]; - } /* end while */ - - /* Check for any stored sequences which need to be flushed */ - if(nseq>0) { - /* Write out the sequence */ - if (H5F_seq_writev(f, dxpl_id, layout, dc_plist, space, - elmt_size, nseq, seq_len_arr, buf_off_arr, src)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); - } /* end if */ - - /* Increment amount of I/O performed */ - iter->hyp.elmt_left-=nelem; - - /* Success! */ - ret_value=nelem; - -done: - if(seq_len_arr!=NULL) - H5FL_ARR_FREE(size_t,seq_len_arr); - if(buf_off_arr!=NULL) - H5FL_ARR_FREE(hsize_t,buf_off_arr); - - FUNC_LEAVE (ret_value); -} /* H5S_hyper_fwrite() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_hyper_fwrite_opt - * - * Purpose: Performs an optimized scatter to the file, based on a regular - * hyperslab (i.e. one which was generated from just one call to - * H5Sselect_hyperslab). - * - * Return: Success: Number of elements copied. - * Failure: 0 - * - * Programmer: Quincey Koziol - * Friday, July 6, 2001 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hsize_t -H5S_hyper_fwrite_opt (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, H5S_sel_iter_t *file_iter, - hsize_t nelmts, hid_t dxpl_id, const void *_buf) -{ - size_t *seq_len_arr=NULL; /* Array of sequence lengths */ - hsize_t *buf_off_arr=NULL; /* Array of dataset offsets */ - size_t nseq=0; /* Number of sequence/offsets stored in the arrays */ - size_t tot_buf_size=0; /* Total number of bytes in buffer */ - - hssize_t offset[H5O_LAYOUT_NDIMS]; /* Offset on disk */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */ - hssize_t wrap[H5O_LAYOUT_NDIMS]; /* Bytes to wrap around at the end of a row */ - hsize_t skip[H5O_LAYOUT_NDIMS]; /* Bytes to skip between blocks */ - hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary block count */ - hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary block offset */ - const uint8_t *buf=_buf; /* Alias for pointer arithmetic */ - const H5S_hyper_dim_t *tdiminfo; /* Local pointer to diminfo information */ - hssize_t fast_dim_start, /* Local copies of fastest changing dimension info */ - fast_dim_offset; - hsize_t fast_dim_stride, /* Local copies of fastest changing dimension info */ - fast_dim_block, - fast_dim_buf_off; - size_t fast_dim_count; - size_t tot_blk_count; /* Total number of blocks left to output */ - size_t act_blk_count; /* Actual number of blocks to output */ - int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int temp_dim; /* Temporary rank holder */ - hsize_t acc; /* Accumulator */ - hsize_t buf_off; /* Current buffer offset for copying memory */ - int i; /* Counters */ - unsigned u; /* Counters */ - int ndims; /* Number of dimensions of dataset */ - size_t actual_write; /* The actual number of elements to write out */ - size_t actual_bytes; /* The actual number of bytes to copy */ - size_t io_left; /* The number of elements left in I/O operation */ - size_t tot_seq; /* The number of sequences filled */ - hsize_t *buf_off_arr_p; /* Pointer into the buffer offset array */ - size_t seq_count; /* Temporary count of sequences left to process */ -#ifndef NO_DUFFS_DEVICE - size_t duffs_index; /* Counting index for Duff's device */ -#endif /* NO_DUFFS_DEVICE */ - size_t vector_size; /* Value for vector size */ - H5P_genplist_t *plist; /* Property list */ - hsize_t ret_value=0; /* Return value */ - - FUNC_ENTER_NOINIT(H5S_hyper_fwrite_opt); - - /* Get the hyperslab vector size */ - if(TRUE!=H5P_isa_class(dxpl_id,H5P_DATASET_XFER) || NULL == (plist = H5I_object(dxpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a file access property list"); - if (H5P_get(plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, 0, "unable to get value"); - - /* Allocate the vector I/O arrays */ - if((seq_len_arr = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate vector I/O array"); - if((buf_off_arr = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate vector I/O array"); - - /* Set the rank of the fastest changing dimension */ - fast_dim=file_space->extent.u.simple.rank-1; - ndims=file_space->extent.u.simple.rank; - - /* initialize row sizes for each dimension */ - for(i=(ndims-1),acc=1; i>=0; i--) { - slab[i]=acc*elmt_size; - acc*=file_space->extent.u.simple.size[i]; - } /* end for */ - - /* Set the number of elements left for I/O */ - H5_ASSIGN_OVERFLOW(io_left,nelmts,hsize_t,size_t); - - /* Check if we stopped in the middle of a sequence of elements */ - if((file_iter->hyp.off[fast_dim]-file_space->select.sel_info.hslab.diminfo[fast_dim].start)%file_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0 || - ((file_iter->hyp.off[fast_dim]!=file_space->select.sel_info.hslab.diminfo[fast_dim].start) && file_space->select.sel_info.hslab.diminfo[fast_dim].stride==1)) { - hsize_t leftover; /* The number of elements left over from the last sequence */ - - /* Calculate the number of elements left in the sequence */ - if(file_space->select.sel_info.hslab.diminfo[fast_dim].stride==1) - leftover=file_space->select.sel_info.hslab.diminfo[fast_dim].block-(file_iter->hyp.off[fast_dim]-file_space->select.sel_info.hslab.diminfo[fast_dim].start); - else - leftover=file_space->select.sel_info.hslab.diminfo[fast_dim].block-((file_iter->hyp.off[fast_dim]-file_space->select.sel_info.hslab.diminfo[fast_dim].start)%file_space->select.sel_info.hslab.diminfo[fast_dim].stride); - - /* Make certain that we don't write too many */ - H5_CHECK_OVERFLOW(leftover,hsize_t,size_t); - actual_write=MIN((size_t)leftover,io_left); - actual_bytes=actual_write*elmt_size; - - /* Copy the location of the point to get */ - HDmemcpy(offset, file_iter->hyp.off,ndims*sizeof(hssize_t)); - offset[ndims] = 0; - - /* Add in the selection offset */ - for(i=0; i<ndims; i++) - offset[i] += file_space->select.offset[i]; - - /* Compute the initial buffer offset */ - for(i=0,buf_off=0; i<ndims; i++) - buf_off+=offset[i]*slab[i]; - - /* Write out the rest of the sequence */ - if (H5F_seq_write(f, dxpl_id, layout, dc_plist, file_space, - elmt_size, actual_bytes, buf_off, buf)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); - - /* Increment the offset of the buffer */ - buf+=actual_bytes; - - /* Decrement the amount left to write */ - io_left-=actual_write; - - /* Advance the point iterator */ - /* If we had enough buffer space to write out the rest of the sequence - * in the fastest changing dimension, move the iterator offset to - * the beginning of the next block to write. Otherwise, just advance - * the iterator in the fastest changing dimension. - */ - if(actual_write==leftover) { - /* Move iterator offset to beginning of next sequence in the fastest changing dimension */ - H5S_hyper_iter_next(file_space,file_iter); - } /* end if */ - else { - file_iter->hyp.off[fast_dim]+=actual_write; /* whole sequence not written out, just advance fastest dimension offset */ - } /* end if */ - } /* end if */ - - /* Now that we've cleared the "remainder" of the previous fastest dimension - * sequence, we must be at the beginning of a sequence, so use the fancy - * algorithm to compute the offsets and run through as many as possible, - * until the buffer runs dry. - */ - if(io_left>0) { /* Just in case the "remainder" above emptied the buffer */ - /* Compute the arrays to perform I/O on */ - /* Copy the location of the point to get */ - HDmemcpy(offset, file_iter->hyp.off,ndims*sizeof(hssize_t)); - offset[ndims] = 0; - - /* Add in the selection offset */ - for(i=0; i<ndims; i++) - offset[i] += file_space->select.offset[i]; - - /* Compute the current "counts" for this location */ - for(i=0; i<ndims; i++) { - if(file_space->select.sel_info.hslab.diminfo[i].stride==1) { - tmp_count[i] = 0; - tmp_block[i] = file_iter->hyp.off[i]-file_space->select.sel_info.hslab.diminfo[i].start; - } /* end if */ - else { - tmp_count[i] = (file_iter->hyp.off[i]-file_space->select.sel_info.hslab.diminfo[i].start)/file_space->select.sel_info.hslab.diminfo[i].stride; - tmp_block[i] = (file_iter->hyp.off[i]-file_space->select.sel_info.hslab.diminfo[i].start)%file_space->select.sel_info.hslab.diminfo[i].stride; - } /* end else */ - } /* end for */ - - /* Compute the initial buffer offset */ - for(i=0,buf_off=0; i<ndims; i++) - buf_off+=offset[i]*slab[i]; - - /* Set the number of elements to write each time */ - H5_ASSIGN_OVERFLOW(actual_write,file_space->select.sel_info.hslab.diminfo[fast_dim].block,hsize_t,size_t); - - /* Set the number of actual bytes */ - actual_bytes=actual_write*elmt_size; - - /* Set the local copy of the diminfo pointer */ - tdiminfo=file_space->select.sel_info.hslab.diminfo; - - /* Set local copies of information for the fastest changing dimension */ - fast_dim_start=tdiminfo[fast_dim].start; - fast_dim_stride=tdiminfo[fast_dim].stride; - fast_dim_block=tdiminfo[fast_dim].block; - fast_dim_buf_off=slab[fast_dim]*fast_dim_stride; - fast_dim_offset=fast_dim_start+file_space->select.offset[fast_dim]; - - /* Compute the number of blocks which would fit into the buffer */ - H5_ASSIGN_OVERFLOW(tot_blk_count,(io_left/fast_dim_block),hsize_t,size_t); - - /* Compute the amount to wrap at the end of each row */ - for(i=0; i<ndims; i++) - wrap[i]=(file_space->extent.u.simple.size[i]-(tdiminfo[i].stride*tdiminfo[i].count))*slab[i]; - - /* Compute the amount to skip between blocks */ - for(i=0; i<ndims; i++) - skip[i]=(tdiminfo[i].stride-tdiminfo[i].block)*slab[i]; - - /* Fill the sequence length array (since they will all be the same for optimized hyperslabs) */ - for(u=0; u<vector_size; u++) - seq_len_arr[u]=actual_bytes; - - /* Write out data until an entire sequence can't be written any longer */ - while(io_left>0) { - /* Reset copy of number of blocks in fastest dimension */ - H5_ASSIGN_OVERFLOW(fast_dim_count,tdiminfo[fast_dim].count-tmp_count[fast_dim],hsize_t,size_t); - - /* Check if this entire row will fit into buffer */ - if(fast_dim_count<=tot_blk_count) { - - /* Entire row of blocks fits into buffer */ - act_blk_count=fast_dim_count; - - /* Loop over all the blocks in the fastest changing dimension */ - while(fast_dim_count>0) { - /* Gather the sequence */ - - /* Compute the number of sequences to fill */ - tot_seq=MIN(vector_size-nseq,fast_dim_count); - - /* Get a copy of the number of sequences to fill */ - seq_count=tot_seq; - - /* Set the pointer to the correct starting array element */ - buf_off_arr_p=&buf_off_arr[nseq]; - -#ifdef NO_DUFFS_DEVICE - /* Fill up the buffer, or finish up the blocks in this dimension */ - while(seq_count>0) { - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - seq_count--; - } /* end while */ -#else /* NO_DUFFS_DEVICE */ - duffs_index = (seq_count + 7) / 8; - switch (seq_count % 8) { - case 0: - do - { - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 7: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 6: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 5: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 4: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 3: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 2: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - case 1: - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - } while (--duffs_index > 0); - } /* end switch */ -#endif /* NO_DUFFS_DEVICE */ - - /* Increment number of array elements used */ - nseq+=tot_seq; - - /* Increment the total number of bytes contained in arrays */ - tot_buf_size += tot_seq*actual_bytes; - - /* Decrement number of blocks left */ - fast_dim_count -= tot_seq; - - /* If the sequence & offset arrays are full, write them out */ - if(nseq>=vector_size) { - /* Write out the sequences */ - if (H5F_seq_writev(f, dxpl_id, layout, dc_plist, file_space, - elmt_size, nseq, seq_len_arr, buf_off_arr, buf)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); - - /* Increment the offset of the destination buffer */ - buf+=tot_buf_size; - - /* Reset the number of bytes & sequences */ - tot_buf_size=0; - nseq=0; - } /* end else */ - } /* end while */ - - /* Decrement number of elements left */ - io_left -= actual_write*act_blk_count; - - /* Decrement number of blocks left */ - tot_blk_count -= act_blk_count; - - /* Increment information to reflect block just processed */ - offset[fast_dim]=fast_dim_offset; /* reset the offset in the fastest dimension */ - tmp_count[fast_dim]=0; - - /* Increment offset in destination buffer */ - buf_off += wrap[fast_dim]; - } /* end if */ - else { - - /* Entire row of blocks doesn't fit into buffer */ - act_blk_count=tot_blk_count; - - /* Reduce number of blocks to output */ - fast_dim_count=tot_blk_count; - - /* Loop over all the blocks in the fastest changing dimension */ - while(fast_dim_count>0) { - /* Gather the sequence */ - - /* Compute the number of sequences to fill */ - tot_seq=MIN(vector_size-nseq,fast_dim_count); - - /* Get a copy of the number of sequences to fill */ - seq_count=tot_seq; - - /* Set the pointer to the correct starting array element */ - buf_off_arr_p=&buf_off_arr[nseq]; - - /* Fill up the buffer, or finish up the blocks in this dimension */ - while(seq_count>0) { - /* Store of length & offset */ - /* seq_len_arr[nseq] already has the correct value */ - *buf_off_arr_p++=buf_off; - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - seq_count--; - } /* end while */ - - /* Increment number of array elements used */ - nseq+=tot_seq; - - /* Increment the total number of bytes contained in arrays */ - tot_buf_size += tot_seq*actual_bytes; - - /* Decrement number of blocks left */ - fast_dim_count -= tot_seq; - - /* If the sequence & offset arrays are full, write them out */ - if(nseq>=vector_size) { - /* Write out the sequences */ - if (H5F_seq_writev(f, dxpl_id, layout, dc_plist, file_space, - elmt_size, nseq, seq_len_arr, buf_off_arr, buf)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); - - /* Increment the offset of the destination buffer */ - buf+=tot_buf_size; - - /* Reset the number of bytes & sequences */ - tot_buf_size=0; - nseq=0; - } /* end else */ - } /* end while */ - - /* Decrement number of elements left */ - io_left -= actual_write*act_blk_count; - - /* Decrement number of blocks left */ - tot_blk_count -= act_blk_count; - - /* Increment information to reflect block just processed */ - offset[fast_dim]+=(fast_dim_stride*act_blk_count); /* reset the offset in the fastest dimension */ - tmp_count[fast_dim]+=act_blk_count; - - /* Handle any leftover, partial blocks in this row */ - if(io_left>0) { - actual_write=io_left; - actual_bytes=actual_write*elmt_size; - - /* Gather the sequence */ - - /* Store of length & offset */ - seq_len_arr[nseq]=actual_bytes; - buf_off_arr[nseq]=buf_off; - - /* Increment the total number of bytes contained in arrays */ - tot_buf_size += actual_bytes; - - /* Increment the number of sequences in arrays */ - nseq++; - - /* If the sequence & offset arrays are full, write them out */ - if(nseq>=vector_size) { - /* Write out the sequences */ - if (H5F_seq_writev(f, dxpl_id, layout, dc_plist, file_space, - elmt_size, nseq, seq_len_arr, buf_off_arr, buf)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); - - /* Increment the offset of the destination buffer */ - buf+=tot_buf_size; - - /* Reset the number of bytes & sequences */ - tot_buf_size=0; - nseq=0; - } /* end else */ - - /* Increment the source offset */ - buf_off+=fast_dim_buf_off; - - /* Decrement the number of elements left */ - io_left -= actual_write; - - /* Increment buffer correctly */ - offset[fast_dim]+=actual_write; - } /* end if */ - - /* don't bother checking slower dimensions */ - assert(tot_blk_count==0); - assert(io_left==0); - break; - } /* end else */ - - /* Increment the offset and count for the other dimensions */ - temp_dim=fast_dim-1; - while(temp_dim>=0) { - /* Move to the next row in the curent dimension */ - offset[temp_dim]++; - tmp_block[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_block[temp_dim]<tdiminfo[temp_dim].block) - break; - else { - /* Move to the next block in the current dimension */ - offset[temp_dim]+=(tdiminfo[temp_dim].stride-tdiminfo[temp_dim].block); - buf_off += skip[temp_dim]; - tmp_block[temp_dim]=0; - tmp_count[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_count[temp_dim]<tdiminfo[temp_dim].count) - break; - else { - offset[temp_dim]=tdiminfo[temp_dim].start+file_space->select.offset[temp_dim]; - buf_off += wrap[temp_dim]; - tmp_count[temp_dim]=0; /* reset back to the beginning of the line */ - tmp_block[temp_dim]=0; - } /* end else */ - } /* end else */ - - /* Decrement dimension count */ - temp_dim--; - } /* end while */ - } /* end while */ - - /* Check for any stored sequences which need to be flushed */ - if(nseq>0) { - /* Write out the sequence */ - if (H5F_seq_writev(f, dxpl_id, layout, dc_plist, file_space, - elmt_size, nseq, seq_len_arr, buf_off_arr, buf)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); - } /* end if */ - - /* Subtract out the selection offset */ - for(i=0; i<ndims; i++) - offset[i] -= file_space->select.offset[i]; - - /* Update the iterator with the location we stopped */ - HDmemcpy(file_iter->hyp.off, offset, ndims*sizeof(hssize_t)); - } /* end if */ - - /* Decrement the number of elements left in selection */ - file_iter->hyp.elmt_left -= (nelmts-io_left); - - ret_value= (nelmts-io_left); - -done: - if(seq_len_arr!=NULL) - H5FL_ARR_FREE(size_t,seq_len_arr); - if(buf_off_arr!=NULL) - H5FL_ARR_FREE(hsize_t,buf_off_arr); - - FUNC_LEAVE (ret_value); -} /* H5S_hyper_fwrite_opt() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_hyper_fscat - * - * Purpose: Scatters dataset elements from the type conversion buffer BUF - * to the file F where the data points are arranged according to - * the file data space FILE_SPACE and stored according to - * LAYOUT and EFL. Each element is ELMT_SIZE bytes. - * The caller is requesting that NELMTS elements are copied. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Tuesday, June 16, 1998 - * - * Modifications: - * Robb Matzke, 1999-08-03 - * The data transfer properties are passed by ID since that's - * what the virtual file layer needs. - *------------------------------------------------------------------------- - */ -static herr_t -H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, H5S_sel_iter_t *file_iter, - hsize_t nelmts, hid_t dxpl_id, const void *_buf) -{ - hsize_t num_written=0; /* number of elements read into buffer */ - herr_t ret_value=SUCCEED; - - FUNC_ENTER_NOAPI(H5S_hyper_fscat, 0); - - /* Check args */ - assert (f); - assert (layout); - assert (elmt_size>0); - assert (file_space); - assert (file_iter); - assert (nelmts>0); - assert (_buf); - - /* Check for the special case of just one H5Sselect_hyperslab call made */ - if(file_space->select.sel_info.hslab.diminfo!=NULL) { - /* Use optimized call to write out regular hyperslab */ - num_written=H5S_hyper_fwrite_opt(f,layout,dc_plist,elmt_size,file_space,file_iter,nelmts,dxpl_id,_buf); - } /* end if */ - else { - /* Perform generic hyperslab operation */ - num_written=H5S_hyper_fwrite(f,layout,dc_plist,elmt_size,file_space,file_iter,nelmts,dxpl_id,_buf); - } /* end else */ - - FUNC_LEAVE (ret_value==FAIL ? ret_value : (num_written >0) ? SUCCEED : FAIL); -} /* H5S_hyper_fscat() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_hyper_mread - * - * Purpose: Performs an optimized gather from a memory buffer, based on a - * hyperslab span selection. - * - * Return: Success: Number of elements copied. - * Failure: 0 - * - * Programmer: Quincey Koziol - * Tuesday, September 12, 2000 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hssize_t -H5S_hyper_mread (const void *_buf, size_t elmt_size, const H5S_t *space, - H5S_sel_iter_t *iter, hsize_t nelem, void *_tconv_buf/*out*/) -{ - const uint8_t *src=(const uint8_t *)_buf; /* Alias for pointer arithmetic */ - const uint8_t *tmp_src; /* Alias for pointer arithmetic */ - uint8_t *dst=(uint8_t *)_tconv_buf; /* Alias for pointer arithmetic */ - H5S_hyper_span_t **ispan; /* Iterator's hyperslab span nodes */ - H5S_hyper_span_t *curr_span; /* Current hyperslab span node */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Cumulative size of each dimension in bytes */ - hsize_t acc; /* Accumulator for computing cumulative sizes */ - hssize_t *abs_arr; /* Absolute hyperslab span position */ - hssize_t *off_arr; /* Offset within the dataspace extent */ - int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int curr_dim; /* Current dimension being operated on */ - int ndims; /* Number of dimensions of dataset */ - size_t span_size=0; /* Number of bytes in current span to actually process */ - size_t io_bytes_left; /* Number of bytes left to process */ - int i; /* Index variable */ - hssize_t ret_value=FAIL; - - FUNC_ENTER_NOINIT(H5S_hyper_mread); - - /* Check args */ - assert(src); - assert(elmt_size>0); - assert(space); - assert(iter); - assert(nelem>0); - assert(dst); - - /* Set the rank of the fastest changing dimension */ - ndims=space->extent.u.simple.rank; - fast_dim=(ndims-1); - - /* Get the pointers to the current span info and span nodes */ - curr_span=iter->hyp.span[fast_dim]; - abs_arr=iter->hyp.off; - off_arr=space->select.offset; - ispan=iter->hyp.span; - - /* Set the amount of elements to perform I/O on, etc. */ - H5_ASSIGN_OVERFLOW(io_bytes_left,nelem*elmt_size,hsize_t,size_t); - - /* Compute the cumulative size of dataspace dimensions */ - for(i=fast_dim, acc=elmt_size; i>=0; i--) { - slab[i]=acc; - acc*=space->extent.u.simple.size[i]; - } /* end for */ - - /* Set the offset of the first element iterated on */ - for(i=0, tmp_src=src; i<ndims; i++) - /* Compute the sequential element offset */ - tmp_src+=(abs_arr[i]+space->select.offset[i])*slab[i]; - - /* Range check against number of elements left in selection */ - assert(io_bytes_left<=(iter->hyp.elmt_left*elmt_size)); - - /* Take care of any partial spans leftover from previous I/Os */ - if(abs_arr[fast_dim]!=curr_span->low) { - - /* Finish the span in the fastest changing dimension */ - - /* Compute the number of bytes to attempt in this span */ - H5_ASSIGN_OVERFLOW(span_size,((curr_span->high-abs_arr[fast_dim])+1)*elmt_size,hsize_t,size_t); - - /* Check number of elements against upper bounds allowed */ - if(span_size>io_bytes_left) - span_size=io_bytes_left; - - HDmemcpy(dst,tmp_src,span_size); - - /* Increment offset in destination */ - dst+=span_size; - - /* Decrement I/O left to perform */ - io_bytes_left-=span_size; - - /* Check if we are done */ - if(io_bytes_left>0) { - /* Move to next span in fastest changing dimension */ - curr_span=curr_span->next; - - if(curr_span!=NULL) { - /* Move location offset of destination */ - tmp_src+=(curr_span->low-abs_arr[fast_dim])*elmt_size; - - /* Move iterator for fastest changing dimension */ - abs_arr[fast_dim]=curr_span->low; - } /* end if */ - } /* end if */ - else { - abs_arr[fast_dim]+=span_size/elmt_size; - - /* Check if we are still within the span */ - if(abs_arr[fast_dim]<=curr_span->high) { - iter->hyp.span[fast_dim]=curr_span; - - goto partial_done; /* finished with partial span */ - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[fast_dim]=curr_span->low; - iter->hyp.span[fast_dim]=curr_span; - - goto partial_done; /* finished with partial span */ - } /* end if */ - } /* end else */ - } /* end else */ - - /* Adjust iterator pointers */ - - if(curr_span==NULL) { -/* Same as code in main loop */ - /* Start at the next fastest dim */ - curr_dim=fast_dim-1; - - /* Work back up through the dimensions */ - while(curr_dim>=0) { - /* Reset the current span */ - curr_span=iter->hyp.span[curr_dim]; - - /* Increment absolute position */ - abs_arr[curr_dim]++; - - /* Check if we are still within the span */ - if(abs_arr[curr_dim]<=curr_span->high) { - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[curr_dim]=curr_span->low; - - break; - } /* end if */ - else { - /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ - curr_dim--; - } /* end else */ - } /* end else */ - } /* end while */ - - /* Check if we are finished with the spans in the tree */ - if(curr_dim<0) { - /* We had better be done with I/O or bad things are going to happen... */ - assert(io_bytes_left==0); - - goto partial_done; /* finished with partial span */ - } /* end if */ - else { - /* Reset the span in the current dimension */ - ispan[curr_dim]=curr_span; - - /* Walk back down the iterator positions, reseting them */ - while(curr_dim<fast_dim) { - assert(curr_span); - assert(curr_span->down); - assert(curr_span->down->head); - - /* Set the new span for this dimension */ - iter->hyp.span[curr_dim+1]=curr_span->down->head; - - /* Advance span down the tree */ - curr_span=curr_span->down->head; - - /* Reset the absolute offset for the dim */ - abs_arr[curr_dim+1]=curr_span->low; - - /* Increment current dimension */ - curr_dim++; - } /* end while */ - - /* Verify that the curr_span points to the fastest dim */ - assert(curr_span==iter->hyp.span[fast_dim]); - } /* end else */ - - /* Reset the buffer offset */ - for(i=0, tmp_src=src; i<ndims; i++) - tmp_src+=(abs_arr[i]+off_arr[i])*slab[i]; - } /* end if */ - } /* end if */ - -partial_done: /* Yes, goto's are evil, so sue me... :-) */ - - /* Perform the I/O on the elements, based on the position of the iterator */ - while(io_bytes_left>0) { - /* Adjust buffer offset of source to compensate for initial increment below */ - tmp_src-=curr_span->pstride; - - /* Loop over all the spans in the fastest changing dimension */ - while(curr_span!=NULL) { - /* Move buffer offset of source */ - tmp_src+=curr_span->pstride; - - /* Compute the number of elements to attempt in this span */ - H5_ASSIGN_OVERFLOW(span_size,curr_span->nelem,hsize_t,size_t); - - /* Check number of elements against upper bounds allowed */ - if(span_size>=io_bytes_left) { - /* Trim the number of bytes to output */ - span_size=io_bytes_left; - io_bytes_left=0; - -/* COMMON */ - /* "Read" the data from the source buffer */ - HDmemcpy(dst,tmp_src,span_size); - - /* Increment offset in destination */ - dst+=span_size; -/* end COMMON */ - - /* Break out now, we are finished with I/O */ - break; - } /* end if */ - else { - /* Decrement I/O left to perform */ - io_bytes_left-=span_size; - -/* COMMON */ - /* "Read" the data from the source buffer */ - HDmemcpy(dst,tmp_src,span_size); - - /* Increment offset in destination */ - dst+=span_size; -/* end COMMON */ - } /* end else */ - - /* Move to next span in fastest changing dimension */ - curr_span=curr_span->next; - } /* end while */ - - /* Check if we are done */ - if(io_bytes_left==0) { - abs_arr[fast_dim]=curr_span->low+(span_size/elmt_size); - - /* Check if we are still within the span */ - if(abs_arr[fast_dim]<=curr_span->high) { - iter->hyp.span[fast_dim]=curr_span; - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[fast_dim]=curr_span->low; - iter->hyp.span[fast_dim]=curr_span; - break; - } /* end if */ - } /* end else */ - } /* end if */ - - /* Adjust iterator pointers */ - - /* Start at the next fastest dim */ - curr_dim=fast_dim-1; - - /* Work back up through the dimensions */ - while(curr_dim>=0) { - /* Reset the current span */ - curr_span=iter->hyp.span[curr_dim]; - - /* Increment absolute position */ - abs_arr[curr_dim]++; - - /* Check if we are still within the span */ - if(abs_arr[curr_dim]<=curr_span->high) { - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[curr_dim]=curr_span->low; - - break; - } /* end if */ - else { - /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ - curr_dim--; - } /* end else */ - } /* end else */ - } /* end while */ - - /* Check if we are finished with the spans in the tree */ - if(curr_dim<0) { - /* We had better be done with I/O or bad things are going to happen... */ - assert(io_bytes_left==0); - break; - } /* end if */ - else { - /* Reset the span in the current dimension */ - ispan[curr_dim]=curr_span; - - /* Walk back down the iterator positions, reseting them */ - while(curr_dim<fast_dim) { - assert(curr_span); - assert(curr_span->down); - assert(curr_span->down->head); - - /* Set the new span for the next dimension down */ - iter->hyp.span[curr_dim+1]=curr_span->down->head; - - /* Advance span down the tree */ - curr_span=curr_span->down->head; - - /* Reset the absolute offset for the dim */ - abs_arr[curr_dim+1]=curr_span->low; - - /* Increment current dimension */ - curr_dim++; - } /* end while */ - - /* Verify that the curr_span points to the fastest dim */ - assert(curr_span==iter->hyp.span[fast_dim]); - } /* end else */ - - /* Reset the buffer offset */ - for(i=0, tmp_src=src; i<ndims; i++) - tmp_src+=(abs_arr[i]+off_arr[i])*slab[i]; - } /* end while */ - - /* Increment amount of I/O performed */ - iter->hyp.elmt_left-=nelem; - - /* Success! */ - ret_value=nelem; - -#ifdef LATER -done: -#endif /* LATER */ - FUNC_LEAVE (ret_value); -} /* end H5S_hyper_mread() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_hyper_mread_opt - * - * Purpose: Performs an optimized gather from a memory buffer, based on a - * regular hyperslab (i.e. one which was generated from just one call to - * H5Sselect_hyperslab). - * - * Return: Success: Number of elements copied. - * Failure: 0 - * - * Programmer: Quincey Koziol - * Tuesday, September 12, 2000 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hsize_t -H5S_hyper_mread_opt (const void *_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *_tconv_buf/*out*/) -{ - hsize_t mem_size[H5O_LAYOUT_NDIMS]; /* Size of the source buffer */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */ - hssize_t wrap[H5O_LAYOUT_NDIMS]; /* Bytes to wrap around at the end of a row */ - hsize_t skip[H5O_LAYOUT_NDIMS]; /* Bytes to skip between blocks */ - hssize_t offset[H5O_LAYOUT_NDIMS]; /* Offset on disk */ - hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary block count */ - hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary block offset */ - const uint8_t *src=(const uint8_t *)_buf; /* Alias for pointer arithmetic */ - uint8_t *dst=(uint8_t *)_tconv_buf; /* Alias for pointer arithmetic */ - const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ - hssize_t fast_dim_start, /* Local copies of fastest changing dimension info */ - fast_dim_offset; - hsize_t fast_dim_stride, /* Local copies of fastest changing dimension info */ - fast_dim_block; - size_t fast_dim_count; - size_t tot_blk_count; /* Total number of blocks left to output */ - size_t act_blk_count; /* Actual number of blocks to output */ - size_t fast_dim_buf_off; /* Local copy of amount to move fastest dimension buffer offset */ - int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int temp_dim; /* Temporary rank holder */ - hsize_t acc; /* Accumulator */ - int i; /* Counters */ - int ndims; /* Number of dimensions of dataset */ - size_t actual_read; /* The actual number of elements to read in */ - size_t actual_bytes; /* The actual number of bytes to copy */ - size_t io_left; /* The number of elements left in I/O operation */ -#ifndef NO_DUFFS_DEVICE - size_t duffs_index; /* Counting index for Duff's device */ -#endif /* NO_DUFFS_DEVICE */ - - FUNC_ENTER_NOINIT(H5S_hyper_mread_opt); - - /* Set the aliases for a few important dimension ranks */ - fast_dim=mem_space->extent.u.simple.rank-1; - ndims=mem_space->extent.u.simple.rank; - - /* Set up the size of the memory space */ - HDmemcpy(mem_size, mem_space->extent.u.simple.size,mem_space->extent.u.simple.rank*sizeof(hsize_t)); - mem_size[mem_space->extent.u.simple.rank]=elmt_size; - - /* initialize row sizes for each dimension */ - for(i=(ndims-1),acc=1; i>=0; i--) { - slab[i]=acc*elmt_size; - acc*=mem_size[i]; - } /* end for */ - - /* Set the number of elements left for I/O */ - H5_ASSIGN_OVERFLOW(io_left,nelmts,hsize_t,size_t); - - /* Check if we stopped in the middle of a sequence of elements */ - if((mem_iter->hyp.off[fast_dim]-mem_space->select.sel_info.hslab.diminfo[fast_dim].start)%mem_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0 || - ((mem_iter->hyp.off[fast_dim]!=mem_space->select.sel_info.hslab.diminfo[fast_dim].start) && mem_space->select.sel_info.hslab.diminfo[fast_dim].stride==1)) { - hsize_t leftover; /* The number of elements left over from the last sequence */ - - /* Calculate the number of elements left in the sequence */ - if(mem_space->select.sel_info.hslab.diminfo[fast_dim].stride==1) - leftover=mem_space->select.sel_info.hslab.diminfo[fast_dim].block-(mem_iter->hyp.off[fast_dim]-mem_space->select.sel_info.hslab.diminfo[fast_dim].start); - else - leftover=mem_space->select.sel_info.hslab.diminfo[fast_dim].block-((mem_iter->hyp.off[fast_dim]-mem_space->select.sel_info.hslab.diminfo[fast_dim].start)%mem_space->select.sel_info.hslab.diminfo[fast_dim].stride); - - /* Make certain that we don't write too many */ - H5_CHECK_OVERFLOW(leftover,hsize_t,size_t); - actual_read=MIN((size_t)leftover,io_left); - actual_bytes=actual_read*elmt_size; - - /* Copy the location of the point to get */ - HDmemcpy(offset, mem_iter->hyp.off,ndims*sizeof(hssize_t)); - offset[ndims] = 0; - - /* Add in the selection offset */ - for(i=0; i<ndims; i++) - offset[i] += mem_space->select.offset[i]; - - /* Compute the initial buffer offset */ - for(i=0,src=_buf; i<ndims; i++) - src+=offset[i]*slab[i]; - - /* Scatter out the rest of the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - dst+=actual_bytes; - - /* Decrement the number of elements written out */ - io_left -= actual_read; - - /* Advance the point iterator */ - /* If we had enough buffer space to read in the rest of the sequence - * in the fastest changing dimension, move the iterator offset to - * the beginning of the next block to read. Otherwise, just advance - * the iterator in the fastest changing dimension. - */ - if(actual_read==leftover) { - /* Move iterator offset to beginning of next sequence in the fastest changing dimension */ - H5S_hyper_iter_next(mem_space,mem_iter); - } /* end if */ - else { - mem_iter->hyp.off[fast_dim]+=actual_read; /* whole sequence not written out, just advance fastest dimension offset */ - } /* end if */ - } /* end if */ - - /* Now that we've cleared the "remainder" of the previous fastest dimension - * sequence, we must be at the beginning of a sequence, so use the fancy - * algorithm to compute the offsets and run through as many as possible, - * until the buffer fills up. - */ - if(io_left>0) { /* Just in case the "remainder" above filled the buffer */ - /* Compute the arrays to perform I/O on */ - /* Copy the location of the point to get */ - HDmemcpy(offset, mem_iter->hyp.off,ndims*sizeof(hssize_t)); - offset[ndims] = 0; - - /* Add in the selection offset */ - for(i=0; i<ndims; i++) - offset[i] += mem_space->select.offset[i]; - - /* Compute the current "counts" for this location */ - for(i=0; i<ndims; i++) { - if(mem_space->select.sel_info.hslab.diminfo[i].stride==1) { - tmp_count[i] = 0; - tmp_block[i] = mem_iter->hyp.off[i]-mem_space->select.sel_info.hslab.diminfo[i].start; - } /* end if */ - else { - tmp_count[i] = (mem_iter->hyp.off[i]-mem_space->select.sel_info.hslab.diminfo[i].start)/mem_space->select.sel_info.hslab.diminfo[i].stride; - tmp_block[i] = (mem_iter->hyp.off[i]-mem_space->select.sel_info.hslab.diminfo[i].start)%mem_space->select.sel_info.hslab.diminfo[i].stride; - } /* end else */ - } /* end for */ - - /* Compute the initial buffer offset */ - for(i=0,src=_buf; i<ndims; i++) - src+=offset[i]*slab[i]; - - /* Set the number of elements to write each time */ - H5_ASSIGN_OVERFLOW(actual_read,mem_space->select.sel_info.hslab.diminfo[fast_dim].block,hsize_t,size_t); - - /* Set the number of actual bytes */ - actual_bytes=actual_read*elmt_size; - - /* Set the local copy of the diminfo pointer */ - tdiminfo=mem_space->select.sel_info.hslab.diminfo; - - /* Set local copies of information for the fastest changing dimension */ - fast_dim_start=tdiminfo[fast_dim].start; - fast_dim_stride=tdiminfo[fast_dim].stride; - fast_dim_block=tdiminfo[fast_dim].block; - H5_ASSIGN_OVERFLOW(fast_dim_buf_off,(slab[fast_dim]*fast_dim_stride),hsize_t,size_t); - fast_dim_offset=fast_dim_start+mem_space->select.offset[fast_dim]; - - /* Compute the number of blocks which would fit into the buffer */ - H5_ASSIGN_OVERFLOW(tot_blk_count,(io_left/fast_dim_block),hsize_t,size_t); - - /* Compute the amount to wrap at the end of each row */ - for(i=0; i<ndims; i++) - wrap[i]=(mem_size[i]-(tdiminfo[i].stride*tdiminfo[i].count))*slab[i]; - - /* Compute the amount to skip between blocks */ - for(i=0; i<ndims; i++) - skip[i]=(tdiminfo[i].stride-tdiminfo[i].block)*slab[i]; - - /* Read in data until an entire sequence can't be written out any longer */ - while(io_left>0) { - /* Reset copy of number of blocks in fastest dimension */ - H5_ASSIGN_OVERFLOW(fast_dim_count,tdiminfo[fast_dim].count-tmp_count[fast_dim],hsize_t,size_t); - - /* Check if this entire row will fit into buffer */ - if(fast_dim_count<=tot_blk_count) { - - /* Entire row of blocks fits into buffer */ - act_blk_count=fast_dim_count; - -#ifdef NO_DUFFS_DEVICE - /* Loop over all the blocks in the fastest changing dimension */ - while(fast_dim_count>0) { - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - dst+=actual_bytes; - - /* Increment information to reflect block just processed */ - src+=fast_dim_buf_off; - - /* Decrement number of blocks */ - fast_dim_count--; - } /* end while */ -#else /* NO_DUFFS_DEVICE */ - duffs_index = (fast_dim_count + 7) / 8; - switch (fast_dim_count % 8) { - case 0: - do - { - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - dst+=actual_bytes; - - /* Increment information to reflect block just processed */ - src+=fast_dim_buf_off; - - case 7: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - dst+=actual_bytes; - - /* Increment information to reflect block just processed */ - src+=fast_dim_buf_off; - - case 6: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - dst+=actual_bytes; - - /* Increment information to reflect block just processed */ - src+=fast_dim_buf_off; - - case 5: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - dst+=actual_bytes; - - /* Increment information to reflect block just processed */ - src+=fast_dim_buf_off; - - case 4: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - dst+=actual_bytes; - - /* Increment information to reflect block just processed */ - src+=fast_dim_buf_off; - - case 3: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - dst+=actual_bytes; - - /* Increment information to reflect block just processed */ - src+=fast_dim_buf_off; - - case 2: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - dst+=actual_bytes; - - /* Increment information to reflect block just processed */ - src+=fast_dim_buf_off; - - case 1: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - dst+=actual_bytes; - - /* Increment information to reflect block just processed */ - src+=fast_dim_buf_off; - - } while (--duffs_index > 0); - } /* end switch */ -#endif /* NO_DUFFS_DEVICE */ - - /* Decrement number of elements left */ - io_left -= actual_read*act_blk_count; - - /* Decrement number of blocks left */ - tot_blk_count -= act_blk_count; - - /* Increment information to reflect block just processed */ - offset[fast_dim]=fast_dim_offset; /* reset the offset in the fastest dimension */ - tmp_count[fast_dim]=0; - - /* Increment offset in destination buffer */ - src += wrap[fast_dim]; - } /* end if */ - else { - - /* Entire row of blocks doesn't fit into buffer */ - act_blk_count=tot_blk_count; - - /* Reduce number of blocks to output */ - fast_dim_count=tot_blk_count; - - /* Loop over all the blocks in the fastest changing dimension */ - while(fast_dim_count>0) { - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - dst+=actual_bytes; - - /* Increment information to reflect block just processed */ - src+=fast_dim_buf_off; - - /* Decrement number of blocks */ - fast_dim_count--; - } /* end while */ - - /* Decrement number of elements left */ - io_left -= actual_read*act_blk_count; - - /* Decrement number of blocks left */ - tot_blk_count -= act_blk_count; - - /* Increment information to reflect block just processed */ - offset[fast_dim]+=(fast_dim_stride*act_blk_count); /* reset the offset in the fastest dimension */ - tmp_count[fast_dim]+=act_blk_count; - - /* Handle any leftover, partial blocks in this row */ - if(io_left>0) { - actual_read=io_left; - actual_bytes=actual_read*elmt_size; - - /* Scatter out the rest of the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - dst+=actual_bytes; - - /* Decrement the number of elements left */ - io_left -= actual_read; - - /* Increment buffer correctly */ - offset[fast_dim]+=actual_read; - } /* end if */ - - /* don't bother checking slower dimensions */ - assert(tot_blk_count==0); - assert(io_left==0); - break; - } /* end else */ - - /* Increment the offset and count for the other dimensions */ - temp_dim=fast_dim-1; - while(temp_dim>=0) { - /* Move to the next row in the curent dimension */ - offset[temp_dim]++; - tmp_block[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_block[temp_dim]<tdiminfo[temp_dim].block) - break; - else { - /* Move to the next block in the current dimension */ - offset[temp_dim]+=(tdiminfo[temp_dim].stride-tdiminfo[temp_dim].block); - src += skip[temp_dim]; - tmp_block[temp_dim]=0; - tmp_count[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_count[temp_dim]<tdiminfo[temp_dim].count) - break; - else { - offset[temp_dim]=tdiminfo[temp_dim].start+mem_space->select.offset[temp_dim]; - src += wrap[temp_dim]; - tmp_count[temp_dim]=0; /* reset back to the beginning of the line */ - tmp_block[temp_dim]=0; - } /* end else */ - } /* end else */ - - /* Decrement dimension count */ - temp_dim--; - } /* end while */ - } /* end while */ - - /* Subtract out the selection offset */ - for(i=0; i<ndims; i++) - offset[i] -= mem_space->select.offset[i]; - - /* Update the iterator with the location we stopped */ - HDmemcpy(mem_iter->hyp.off, offset, ndims*sizeof(hssize_t)); - } /* end if */ - - /* Decrement the number of elements left in selection */ - mem_iter->hyp.elmt_left-=(nelmts-io_left); - - FUNC_LEAVE (nelmts-io_left); -} /* end H5S_hyper_mread_opt() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_hyper_mgath - * - * Purpose: Gathers dataset elements from application memory BUF and - * copies them into the data type conversion buffer TCONV_BUF. - * Each element is ELMT_SIZE bytes and arranged in application - * memory according to MEM_SPACE. - * The caller is requesting that at most NELMTS be gathered. - * - * Return: Success: Number of elements copied. - * - * Failure: 0 - * - * Programmer: Quincey Koziol - * Tuesday, June 16, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hsize_t -H5S_hyper_mgath (const void *_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *_tconv_buf/*out*/) -{ - hsize_t num_read; /* number of elements read into buffer */ - - FUNC_ENTER_NOAPI(H5S_hyper_mgath, 0); - - /* Check args */ - assert (elmt_size>0); - assert (mem_space); - assert (mem_iter); - assert (nelmts>0); - assert (_buf); - assert (_tconv_buf); - - /* Check for the special case of just one H5Sselect_hyperslab call made */ - if(mem_space->select.sel_info.hslab.diminfo!=NULL) { - /* Use optimized call to read in regular hyperslab */ - num_read=H5S_hyper_mread_opt(_buf,elmt_size,mem_space,mem_iter,nelmts,_tconv_buf); - } /* end if */ - else { - /* Perform generic hyperslab operation */ - num_read=H5S_hyper_mread(_buf,elmt_size,mem_space,mem_iter,nelmts,_tconv_buf); - } /* end else */ - - FUNC_LEAVE (num_read); -} /* H5S_hyper_mgath() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_hyper_mwrite - * - * Purpose: Performs an optimized gather from a memory buffer, based on a - * hyperslab span selection. - * - * Return: Success: Number of elements copied. - * Failure: 0 - * - * Programmer: Quincey Koziol - * Tuesday, September 12, 2000 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hssize_t -H5S_hyper_mwrite (const void *_tconv_buf, size_t elmt_size, const H5S_t *space, - H5S_sel_iter_t *iter, hsize_t nelem, void *_buf/*out*/) -{ - const uint8_t *src=(const uint8_t *)_tconv_buf; /* Alias for pointer arithmetic */ - uint8_t *dst=(uint8_t *)_buf; /* Alias for pointer arithmetic */ - uint8_t *tmp_dst; /* Alias for pointer arithmetic */ - H5S_hyper_span_t **ispan; /* Iterator's hyperslab span nodes */ - H5S_hyper_span_t *curr_span; /* Current hyperslab span node */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Cumulative size of each dimension in bytes */ - hsize_t acc; /* Accumulator for computing cumulative sizes */ - hssize_t *abs_arr; /* Absolute hyperslab span position */ - hssize_t *off_arr; /* Offset within the dataspace extent */ - int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int curr_dim; /* Current dimension being operated on */ - int ndims; /* Number of dimensions of dataset */ - size_t span_size=0; /* Number of bytes in current span to actually process */ - size_t io_bytes_left; /* Number of bytes left to process */ - int i; /* Index variable */ - hssize_t ret_value=FAIL; - - FUNC_ENTER_NOINIT(H5S_hyper_mwrite); - - /* Check args */ - assert(src); - assert(elmt_size>0); - assert(space); - assert(iter); - assert(nelem>0); - assert(dst); - - /* Set the rank of the fastest changing dimension */ - ndims=space->extent.u.simple.rank; - fast_dim=(ndims-1); - - /* Get the pointers to the current span info and span nodes */ - curr_span=iter->hyp.span[fast_dim]; - abs_arr=iter->hyp.off; - off_arr=space->select.offset; - ispan=iter->hyp.span; - - /* Set the amount of elements to perform I/O on, etc. */ - H5_ASSIGN_OVERFLOW(io_bytes_left,nelem*elmt_size,hsize_t,size_t); - - /* Compute the cumulative size of dataspace dimensions */ - for(i=fast_dim, acc=elmt_size; i>=0; i--) { - slab[i]=acc; - acc*=space->extent.u.simple.size[i]; - } /* end for */ - - /* Set the offset of the first element iterated on */ - for(i=0, tmp_dst=dst; i<ndims; i++) - /* Compute the sequential element offset */ - tmp_dst+=(abs_arr[i]+space->select.offset[i])*slab[i]; - - /* Range check against number of elements left in selection */ - assert(io_bytes_left<=(iter->hyp.elmt_left*elmt_size)); - - /* Take care of any partial spans leftover from previous I/Os */ - if(abs_arr[fast_dim]!=curr_span->low) { - - /* Finish the span in the fastest changing dimension */ - - /* Compute the number of bytes to attempt in this span */ - H5_ASSIGN_OVERFLOW(span_size,((curr_span->high-abs_arr[fast_dim])+1)*elmt_size,hsize_t,size_t); - - /* Check number of elements against upper bounds allowed */ - if(span_size>io_bytes_left) - span_size=io_bytes_left; - - HDmemcpy(tmp_dst,src,span_size); - - /* Increment offset in destination */ - src+=span_size; - - /* Decrement I/O left to perform */ - io_bytes_left-=span_size; - - /* Check if we are done */ - if(io_bytes_left>0) { - /* Move to next span in fastest changing dimension */ - curr_span=curr_span->next; - - if(curr_span!=NULL) { - /* Move location offset of destination */ - tmp_dst+=(curr_span->low-abs_arr[fast_dim])*elmt_size; - - /* Move iterator for fastest changing dimension */ - abs_arr[fast_dim]=curr_span->low; - } /* end if */ - } /* end if */ - else { - abs_arr[fast_dim]+=span_size/elmt_size; - - /* Check if we are still within the span */ - if(abs_arr[fast_dim]<=curr_span->high) { - iter->hyp.span[fast_dim]=curr_span; - - goto partial_done; /* finished with partial span */ - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[fast_dim]=curr_span->low; - iter->hyp.span[fast_dim]=curr_span; - - goto partial_done; /* finished with partial span */ - } /* end if */ - } /* end else */ - } /* end else */ - - /* Adjust iterator pointers */ - - if(curr_span==NULL) { -/* Same as code in main loop */ - /* Start at the next fastest dim */ - curr_dim=fast_dim-1; - - /* Work back up through the dimensions */ - while(curr_dim>=0) { - /* Reset the current span */ - curr_span=iter->hyp.span[curr_dim]; - - /* Increment absolute position */ - abs_arr[curr_dim]++; - - /* Check if we are still within the span */ - if(abs_arr[curr_dim]<=curr_span->high) { - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[curr_dim]=curr_span->low; - - break; - } /* end if */ - else { - /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ - curr_dim--; - } /* end else */ - } /* end else */ - } /* end while */ - - /* Check if we are finished with the spans in the tree */ - if(curr_dim<0) { - /* We had better be done with I/O or bad things are going to happen... */ - assert(io_bytes_left==0); - - goto partial_done; /* finished with partial span */ - } /* end if */ - else { - /* Reset the span in the current dimension */ - ispan[curr_dim]=curr_span; - - /* Walk back down the iterator positions, reseting them */ - while(curr_dim<fast_dim) { - assert(curr_span); - assert(curr_span->down); - assert(curr_span->down->head); - - /* Set the new span_info & span for this dimension */ - iter->hyp.span[curr_dim+1]=curr_span->down->head; - - /* Advance span down the tree */ - curr_span=curr_span->down->head; - - /* Reset the absolute offset for the dim */ - abs_arr[curr_dim+1]=curr_span->low; - - /* Increment current dimension */ - curr_dim++; - } /* end while */ - - /* Verify that the curr_span points to the fastest dim */ - assert(curr_span==iter->hyp.span[fast_dim]); - } /* end else */ - - /* Reset the buffer offset */ - for(i=0, tmp_dst=dst; i<ndims; i++) - tmp_dst+=(abs_arr[i]+off_arr[i])*slab[i]; - } /* end if */ - } /* end if */ - -partial_done: /* Yes, goto's are evil, so sue me... :-) */ - - /* Perform the I/O on the elements, based on the position of the iterator */ - while(io_bytes_left>0) { - /* Adjust buffer offset of destination to compensate for initial increment below */ - tmp_dst-=(size_t)curr_span->pstride; - - /* Loop over all the spans in the fastest changing dimension */ - while(curr_span!=NULL) { - /* Move buffer offset of destination */ - tmp_dst+=(size_t)curr_span->pstride; - - /* Compute the number of elements to attempt in this span */ - H5_ASSIGN_OVERFLOW(span_size,curr_span->nelem,hsize_t,size_t); - - /* Check number of elements against upper bounds allowed */ - if(span_size>=io_bytes_left) { - /* Trim the number of bytes to output */ - span_size=io_bytes_left; - io_bytes_left=0; - -/* COMMON */ - /* "Write" the data into the destination buffer */ - HDmemcpy(tmp_dst,src,span_size); - - /* Increment offset in destination */ - src+=span_size; -/* end COMMON */ - - /* Break out now, we are finished with I/O */ - break; - } /* end if */ - else { - /* Decrement I/O left to perform */ - io_bytes_left-=span_size; - -/* COMMON */ - /* "Write" the data into the destination buffer */ - HDmemcpy(tmp_dst,src,span_size); - - /* Increment offset in destination */ - src+=span_size; -/* end COMMON */ - } /* end else */ - - /* Move to next span in fastest changing dimension */ - curr_span=curr_span->next; - } /* end while */ - - /* Check if we are done */ - if(io_bytes_left==0) { - abs_arr[fast_dim]=curr_span->low+(span_size/elmt_size); - - /* Check if we are still within the span */ - if(abs_arr[fast_dim]<=curr_span->high) { - iter->hyp.span[fast_dim]=curr_span; - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[fast_dim]=curr_span->low; - iter->hyp.span[fast_dim]=curr_span; - break; - } /* end if */ - } /* end else */ - } /* end if */ - - /* Adjust iterator pointers */ - - /* Start at the next fastest dim */ - curr_dim=fast_dim-1; - - /* Work back up through the dimensions */ - while(curr_dim>=0) { - /* Reset the current span */ - curr_span=iter->hyp.span[curr_dim]; - - /* Increment absolute position */ - abs_arr[curr_dim]++; - - /* Check if we are still within the span */ - if(abs_arr[curr_dim]<=curr_span->high) { - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[curr_dim]=curr_span->low; - - break; - } /* end if */ - else { - /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ - curr_dim--; - } /* end else */ - } /* end else */ - } /* end while */ - - /* Check if we are finished with the spans in the tree */ - if(curr_dim<0) { - /* We had better be done with I/O or bad things are going to happen... */ - assert(io_bytes_left==0); - break; - } /* end if */ - else { - /* Reset the span in the current dimension */ - ispan[curr_dim]=curr_span; - - /* Walk back down the iterator positions, reseting them */ - while(curr_dim<fast_dim) { - assert(curr_span); - assert(curr_span->down); - assert(curr_span->down->head); - - /* Set the new span_info & span for the next dimension down */ - iter->hyp.span[curr_dim+1]=curr_span->down->head; - - /* Advance span down the tree */ - curr_span=curr_span->down->head; - - /* Reset the absolute offset for the dim */ - abs_arr[curr_dim+1]=curr_span->low; - - /* Increment current dimension */ - curr_dim++; - } /* end while */ - - /* Verify that the curr_span points to the fastest dim */ - assert(curr_span==iter->hyp.span[fast_dim]); - } /* end else */ - - /* Reset the buffer offset */ - for(i=0, tmp_dst=dst; i<ndims; i++) - tmp_dst+=(abs_arr[i]+off_arr[i])*slab[i]; - } /* end while */ - - /* Increment amount of I/O performed */ - iter->hyp.elmt_left-=nelem; - - /* Success! */ - ret_value=nelem; - -#ifdef LATER -done: -#endif /* LATER */ - FUNC_LEAVE (ret_value); -} /* end H5S_hyper_mwrite() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_hyper_mwrite_opt - * - * Purpose: Performs an optimized scatter to a memory buffer, based on a - * regular hyperslab (i.e. one which was generated from just one call to - * H5Sselect_hyperslab). - * - * Return: Success: Number of elements copied. - * Failure: 0 - * - * Programmer: Quincey Koziol - * Tuesday, September 12, 2000 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hsize_t -H5S_hyper_mwrite_opt (const void *_tconv_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *_buf/*out*/) -{ - hsize_t mem_size[H5O_LAYOUT_NDIMS]; /* Size of the source buffer */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */ - hssize_t wrap[H5O_LAYOUT_NDIMS]; /* Bytes to wrap around at the end of a row */ - hsize_t skip[H5O_LAYOUT_NDIMS]; /* Bytes to skip between blocks */ - hssize_t offset[H5O_LAYOUT_NDIMS]; /* Offset on disk */ - hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary block count */ - hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary block offset */ - const uint8_t *src=(const uint8_t *)_tconv_buf; /* Alias for pointer arithmetic */ - uint8_t *dst=(uint8_t *)_buf; /* Alias for pointer arithmetic */ - const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ - hssize_t fast_dim_start, /* Local copies of fastest changing dimension info */ - fast_dim_offset; - hsize_t fast_dim_stride, /* Local copies of fastest changing dimension info */ - fast_dim_block; - size_t fast_dim_count; - size_t tot_blk_count; /* Total number of blocks left to output */ - size_t act_blk_count; /* Actual number of blocks to output */ - size_t fast_dim_buf_off; /* Local copy of amount to move fastest dimension buffer offset */ - int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int temp_dim; /* Temporary rank holder */ - hsize_t acc; /* Accumulator */ - int i; /* Counters */ - int ndims; /* Number of dimensions of dataset */ - size_t actual_write; /* The actual number of elements to read in */ - size_t actual_bytes; /* The actual number of bytes to copy */ - size_t io_left; /* The number of elements left in I/O operation */ -#ifndef NO_DUFFS_DEVICE - size_t duffs_index; /* Counting index for Duff's device */ -#endif /* NO_DUFFS_DEVICE */ - - FUNC_ENTER_NOINIT(H5S_hyper_mwrite_opt); - - /* Set the aliases for a few important dimension ranks */ - fast_dim=mem_space->extent.u.simple.rank-1; - ndims=mem_space->extent.u.simple.rank; - - /* Set up the size of the memory space */ - HDmemcpy(mem_size, mem_space->extent.u.simple.size,mem_space->extent.u.simple.rank*sizeof(hsize_t)); - mem_size[mem_space->extent.u.simple.rank]=elmt_size; - - /* initialize row sizes for each dimension */ - for(i=(ndims-1),acc=1; i>=0; i--) { - slab[i]=acc*elmt_size; - acc*=mem_size[i]; - } /* end for */ - - /* Set the number of elements left for I/O */ - H5_ASSIGN_OVERFLOW(io_left,nelmts,hsize_t,size_t); - - /* Check if we stopped in the middle of a sequence of elements */ - if((mem_iter->hyp.off[fast_dim]-mem_space->select.sel_info.hslab.diminfo[fast_dim].start)%mem_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0 || - ((mem_iter->hyp.off[fast_dim]!=mem_space->select.sel_info.hslab.diminfo[fast_dim].start) && mem_space->select.sel_info.hslab.diminfo[fast_dim].stride==1)) { - hsize_t leftover; /* The number of elements left over from the last sequence */ - - /* Calculate the number of elements left in the sequence */ - if(mem_space->select.sel_info.hslab.diminfo[fast_dim].stride==1) - leftover=mem_space->select.sel_info.hslab.diminfo[fast_dim].block-(mem_iter->hyp.off[fast_dim]-mem_space->select.sel_info.hslab.diminfo[fast_dim].start); - else - leftover=mem_space->select.sel_info.hslab.diminfo[fast_dim].block-((mem_iter->hyp.off[fast_dim]-mem_space->select.sel_info.hslab.diminfo[fast_dim].start)%mem_space->select.sel_info.hslab.diminfo[fast_dim].stride); - - /* Make certain that we don't write too many */ - H5_CHECK_OVERFLOW(leftover,hsize_t,size_t); - actual_write=MIN((size_t)leftover,io_left); - actual_bytes=actual_write*elmt_size; - - /* Copy the location of the point to get */ - HDmemcpy(offset, mem_iter->hyp.off,ndims*sizeof(hssize_t)); - offset[ndims] = 0; - - /* Add in the selection offset */ - for(i=0; i<ndims; i++) - offset[i] += mem_space->select.offset[i]; - - /* Compute the initial buffer offset */ - for(i=0,dst=(unsigned char *)_buf; i<ndims; i++) - dst+=offset[i]*slab[i]; - - /* Scatter out the rest of the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - src+=actual_bytes; - - /* Decrement the number of elements written out */ - io_left -= actual_write; - - /* Advance the point iterator */ - /* If we had enough buffer space to write out the rest of the sequence - * in the fastest changing dimension, move the iterator offset to - * the beginning of the next block to write. Otherwise, just advance - * the iterator in the fastest changing dimension. - */ - if(actual_write==leftover) { - /* Move iterator offset to beginning of next sequence in the fastest changing dimension */ - H5S_hyper_iter_next(mem_space,mem_iter); - } /* end if */ - else { - mem_iter->hyp.off[fast_dim]+=actual_write; /* whole sequence not written out, just advance fastest dimension offset */ - } /* end if */ - } /* end if */ - - /* Now that we've cleared the "remainder" of the previous fastest dimension - * sequence, we must be at the beginning of a sequence, so use the fancy - * algorithm to compute the offsets and run through as many as possible, - * until the buffer fills up. - */ - if(io_left>0) { /* Just in case the "remainder" above filled the buffer */ - /* Compute the arrays to perform I/O on */ - /* Copy the location of the point to get */ - HDmemcpy(offset, mem_iter->hyp.off,ndims*sizeof(hssize_t)); - offset[ndims] = 0; - - /* Add in the selection offset */ - for(i=0; i<ndims; i++) - offset[i] += mem_space->select.offset[i]; - - /* Compute the current "counts" for this location */ - for(i=0; i<ndims; i++) { - if(mem_space->select.sel_info.hslab.diminfo[i].stride==1) { - tmp_count[i] = 0; - tmp_block[i] = mem_iter->hyp.off[i]-mem_space->select.sel_info.hslab.diminfo[i].start; - } /* end if */ - else { - tmp_count[i] = (mem_iter->hyp.off[i]-mem_space->select.sel_info.hslab.diminfo[i].start)/mem_space->select.sel_info.hslab.diminfo[i].stride; - tmp_block[i] = (mem_iter->hyp.off[i]-mem_space->select.sel_info.hslab.diminfo[i].start)%mem_space->select.sel_info.hslab.diminfo[i].stride; - } /* end else */ - } /* end for */ - - /* Compute the initial buffer offset */ - for(i=0,dst=(unsigned char *)_buf; i<ndims; i++) - dst+=offset[i]*slab[i]; - - /* Set the number of elements to write each time */ - H5_ASSIGN_OVERFLOW(actual_write,mem_space->select.sel_info.hslab.diminfo[fast_dim].block,hsize_t,size_t); - - /* Set the number of actual bytes */ - actual_bytes=actual_write*elmt_size; - - /* Set the local copy of the diminfo pointer */ - tdiminfo=mem_space->select.sel_info.hslab.diminfo; - - /* Set local copies of information for the fastest changing dimension */ - fast_dim_start=tdiminfo[fast_dim].start; - fast_dim_stride=tdiminfo[fast_dim].stride; - fast_dim_block=tdiminfo[fast_dim].block; - H5_ASSIGN_OVERFLOW(fast_dim_buf_off,slab[fast_dim]*fast_dim_stride,hsize_t,size_t); - fast_dim_offset=fast_dim_start+mem_space->select.offset[fast_dim]; - - /* Compute the number of blocks which would fit into the buffer */ - H5_ASSIGN_OVERFLOW(tot_blk_count,(io_left/fast_dim_block),hsize_t,size_t); - - /* Compute the amount to wrap at the end of each row */ - for(i=0; i<ndims; i++) - wrap[i]=(mem_size[i]-(tdiminfo[i].stride*tdiminfo[i].count))*slab[i]; - - /* Compute the amount to skip between blocks */ - for(i=0; i<ndims; i++) - skip[i]=(tdiminfo[i].stride-tdiminfo[i].block)*slab[i]; - - /* Read in data until an entire sequence can't be written out any longer */ - while(io_left>0) { - /* Reset copy of number of blocks in fastest dimension */ - H5_ASSIGN_OVERFLOW(fast_dim_count,tdiminfo[fast_dim].count-tmp_count[fast_dim],hsize_t,size_t); - - /* Check if this entire row will fit into buffer */ - if(fast_dim_count<=tot_blk_count) { - - /* Entire row of blocks fits into buffer */ - act_blk_count=fast_dim_count; - -#ifdef NO_DUFFS_DEVICE - /* Loop over all the blocks in the fastest changing dimension */ - while(fast_dim_count>0) { - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - src+=actual_bytes; - - /* Increment information to reflect block just processed */ - dst+=fast_dim_buf_off; - - /* Decrement number of blocks */ - fast_dim_count--; - } /* end while */ -#else /* NO_DUFFS_DEVICE */ - duffs_index = (fast_dim_count + 7) / 8; - switch (fast_dim_count % 8) { - case 0: - do - { - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - src+=actual_bytes; - - /* Increment information to reflect block just processed */ - dst+=fast_dim_buf_off; - - case 7: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - src+=actual_bytes; - - /* Increment information to reflect block just processed */ - dst+=fast_dim_buf_off; - - case 6: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - src+=actual_bytes; - - /* Increment information to reflect block just processed */ - dst+=fast_dim_buf_off; - - case 5: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - src+=actual_bytes; - - /* Increment information to reflect block just processed */ - dst+=fast_dim_buf_off; - - case 4: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - src+=actual_bytes; - - /* Increment information to reflect block just processed */ - dst+=fast_dim_buf_off; - - case 3: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - src+=actual_bytes; - - /* Increment information to reflect block just processed */ - dst+=fast_dim_buf_off; - - case 2: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - src+=actual_bytes; - - /* Increment information to reflect block just processed */ - dst+=fast_dim_buf_off; - - case 1: - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - src+=actual_bytes; - - /* Increment information to reflect block just processed */ - dst+=fast_dim_buf_off; - - } while (--duffs_index > 0); - } /* end switch */ -#endif /* NO_DUFFS_DEVICE */ - - /* Decrement number of elements left */ - io_left -= actual_write*act_blk_count; - - /* Decrement number of blocks left */ - tot_blk_count -= act_blk_count; - - /* Increment information to reflect block just processed */ - offset[fast_dim]=fast_dim_offset; /* reset the offset in the fastest dimension */ - tmp_count[fast_dim]=0; - - /* Increment offset in destination buffer */ - dst += wrap[fast_dim]; - } /* end if */ - else { - - /* Entire row of blocks doesn't fit into buffer */ - act_blk_count=tot_blk_count; - - /* Reduce number of blocks to output */ - fast_dim_count=tot_blk_count; - - /* Loop over all the blocks in the fastest changing dimension */ - while(fast_dim_count>0) { - /* Scatter out the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - src+=actual_bytes; - - /* Increment information to reflect block just processed */ - dst+=fast_dim_buf_off; - - /* Decrement number of blocks */ - fast_dim_count--; - } /* end while */ - - /* Decrement number of elements left */ - io_left -= actual_write*act_blk_count; - - /* Decrement number of blocks left */ - tot_blk_count -= act_blk_count; - - /* Increment information to reflect block just processed */ - offset[fast_dim]+=(fast_dim_stride*act_blk_count); /* reset the offset in the fastest dimension */ - tmp_count[fast_dim]+=act_blk_count; - - /* Handle any leftover, partial blocks in this row */ - if(io_left>0) { - actual_write=io_left; - actual_bytes=actual_write*elmt_size; - - /* Scatter out the rest of the sequence */ - HDmemcpy(dst,src,actual_bytes); - - /* Increment the offset of the buffer */ - src+=actual_bytes; - - /* Decrement the number of elements left */ - io_left -= actual_write; - - /* Increment buffer correctly */ - offset[fast_dim]+=actual_write; - } /* end if */ - - /* don't bother checking slower dimensions */ - assert(tot_blk_count==0); - assert(io_left==0); - break; - } /* end else */ - - /* Increment the offset and count for the other dimensions */ - temp_dim=fast_dim-1; - while(temp_dim>=0) { - /* Move to the next row in the curent dimension */ - offset[temp_dim]++; - tmp_block[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_block[temp_dim]<tdiminfo[temp_dim].block) - break; - else { - /* Move to the next block in the current dimension */ - offset[temp_dim]+=(tdiminfo[temp_dim].stride-tdiminfo[temp_dim].block); - dst += skip[temp_dim]; - tmp_block[temp_dim]=0; - tmp_count[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_count[temp_dim]<tdiminfo[temp_dim].count) - break; - else { - offset[temp_dim]=tdiminfo[temp_dim].start+mem_space->select.offset[temp_dim]; - dst += wrap[temp_dim]; - tmp_count[temp_dim]=0; /* reset back to the beginning of the line */ - tmp_block[temp_dim]=0; - } /* end else */ - } /* end else */ - - /* Decrement dimension count */ - temp_dim--; - } /* end while */ - } /* end while */ - - /* Subtract out the selection offset */ - for(i=0; i<ndims; i++) - offset[i] -= mem_space->select.offset[i]; - - /* Update the iterator with the location we stopped */ - HDmemcpy(mem_iter->hyp.off, offset, ndims*sizeof(hssize_t)); - } /* end if */ - - /* Decrement the number of elements left in selection */ - mem_iter->hyp.elmt_left-=(nelmts-io_left); - - FUNC_LEAVE (nelmts-io_left); -} /* end H5S_hyper_mwrite_opt() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_hyper_mscat - * - * Purpose: Scatters NELMTS data points from the type conversion buffer - * TCONV_BUF to the application buffer BUF. Each element is - * ELMT_SIZE bytes and they are organized in application memory - * according to MEM_SPACE. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Wednesday, June 17, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static herr_t -H5S_hyper_mscat (const void *_tconv_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *_buf/*out*/) -{ - hsize_t num_written; /* number of elements written into buffer */ - - FUNC_ENTER_NOAPI(H5S_hyper_mscat, 0); - - /* Check args */ - assert (elmt_size>0); - assert (mem_space); - assert (mem_iter); - assert (nelmts>0); - assert (_buf); - assert (_tconv_buf); - - /* Check for the special case of just one H5Sselect_hyperslab call made */ - if(mem_space->select.sel_info.hslab.diminfo!=NULL) { - /* Use optimized call to write out regular hyperslab */ - num_written=H5S_hyper_mwrite_opt(_tconv_buf,elmt_size,mem_space,mem_iter,nelmts,_buf); - } /* end if */ - else { - /* Perform generic hyperslab operation */ - num_written=H5S_hyper_mwrite(_tconv_buf,elmt_size,mem_space,mem_iter,nelmts,_buf); - } /* end else */ - - FUNC_LEAVE (num_written>0 ? SUCCEED : FAIL); -} /* H5S_hyper_mscat() */ - - /*-------------------------------------------------------------------------- NAME H5S_hyper_npoints @@ -4874,7 +1206,7 @@ H5S_hyper_select_valid (const H5S_t *space) Count the number of blocks in a span tree USAGE hssize_t H5S_hyper_span_nblocks(spans) - const H5S_hyper_span_info_t *spans; IN: Hyperslan span tree to count elements of + const H5S_hyper_span_info_t *spans; IN: Hyperslab span tree to count elements of RETURNS Number of blocks in span tree on success; negative on failure DESCRIPTION @@ -5840,475 +2172,6 @@ H5S_hyper_select_regular(const H5S_t *space) /*-------------------------------------------------------------------------- NAME - H5S_hyper_select_iterate_mem_gen - PURPOSE - Internal routine to iterate over the elements of a span tree hyperslab selection - USAGE - herr_t H5S_hyper_select_iterate_mem_gen(iter_info) - H5S_hyper_iter_info_t *iter_info; IN/OUT: Block of iteration parameters to pass into recursive calls - RETURNS - Non-negative on success, negative on failure - DESCRIPTION - Iterates over the elements in a hyperslab span tree selection, calling a - user's callback routine for each element. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5S_hyper_select_iterate_mem_gen(H5S_hyper_iter_info_t *iter_info) -{ - const H5S_t *space; /* Dataspace operating with */ - H5S_sel_iter_t *iter; /* Selection iterator */ - H5S_hyper_span_t *curr_span; /* Current hyperslab span node */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Cumulative size of each dimension in bytes */ - hsize_t acc; /* Accumulator for computing cumulative sizes */ - hssize_t off_arr[H5O_LAYOUT_NDIMS]; /* Current hyperslab span position */ - hssize_t coord_arr[H5O_LAYOUT_NDIMS]; /* Current coordinate position */ - int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int curr_dim; /* Current dimension being operated on */ - int ndims; /* Number of dimensions of dataset */ - hsize_t span_io; /* Number of elements in current span to actually process */ - herr_t user_ret=0; /* User's return value */ - uint8_t *loc; /* Current element location pointer */ - hsize_t loc_off; /* Element offset in the dataspace */ - int i; /* Index variable */ - unsigned u; /* Index variable */ - herr_t ret_value=FAIL; - - FUNC_ENTER_NOINIT(H5S_hyper_select_iterate_mem_gen); - - /* Check args */ - assert(iter_info); - - /* Retrieve some information from the interation info */ - space=iter_info->space; - iter=iter_info->iter; - - /* Set the rank of the fastest changing dimension */ - ndims=space->extent.u.simple.rank; - fast_dim=(ndims-1); - - /* Get the pointers to the current span info and span nodes */ - curr_span=iter->hyp.span[fast_dim]; - - /* Compute the cumulative size of dataspace dimensions */ - for(i=fast_dim, acc=iter_info->elem_size; i>=0; i--) { - slab[i]=acc; - acc*=space->extent.u.simple.size[i]; - } /* end for */ - - /* Set the offset of the first element iterated on */ - for(i=0, loc_off=0; i<ndims; i++) { - /* Set the location */ - off_arr[i]=iter->hyp.span[i]->low; - coord_arr[i]=off_arr[i]+space->select.offset[i]; - - /* Compute the sequential element offset */ - loc_off+=coord_arr[i]*slab[i]; - } /* end for */ - - /* Perform the I/O on the elements, based on the position of the iterator */ - user_ret=0; - while(curr_span!=NULL && user_ret==0) { - /* Compute the number of elements to attempt in this span */ - span_io=(curr_span->high-curr_span->low)+1; - - /* Iterate through all the span elements */ - for(u=0, loc=(uint8_t *)iter_info->src+loc_off; u<span_io && user_ret==0; u++) { - /* Call the user's callback routine */ - user_ret=(*(iter_info->op))(loc,iter_info->dt,(hsize_t)ndims,coord_arr,iter_info->op_data); - - /* Increment the element location */ - off_arr[fast_dim]++; - coord_arr[fast_dim]++; - - /* Increment the buffer offset */ - loc+=slab[fast_dim]; - } /* end for */ - - /* Get out now for user return values not zero */ - if(user_ret!=0) - break; - - /* Adjust iterator pointers */ - - /* Advance span in fastest dimension */ - curr_span=curr_span->next; - - /* See if we are still in the fastest changing dimension */ - if(curr_span!=NULL) { - /* Move the buffer offset */ - loc_off+=(span_io+(curr_span->low-off_arr[fast_dim]))*iter_info->elem_size; - - /* Move the element location */ - off_arr[fast_dim]=curr_span->low; - coord_arr[fast_dim]=off_arr[fast_dim]+space->select.offset[fast_dim]; - } /* end if */ - /* We walked off the spans for the fastest dimension, work our way back up */ - else { - /* Start at the fastest dim */ - curr_dim=fast_dim-1; - - /* Get the pointer to the correct dimension */ - curr_span=iter->hyp.span[curr_dim]; - - /* Work back up through the dimensions */ - while(curr_dim>=0) { - /* Increment position in span */ - off_arr[curr_dim]++; - coord_arr[curr_dim]++; - - /* Check if we are still within the span */ - if(off_arr[curr_dim]<=curr_span->high) { - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset the offset for the dim */ - off_arr[curr_dim]=curr_span->low; - coord_arr[curr_dim]=off_arr[curr_dim]+space->select.offset[curr_dim]; - - break; - } /* end if */ - else { - /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ - curr_dim--; - - /* Reset the curr_span to the next dim */ - if(curr_dim>=0) - curr_span=iter->hyp.span[curr_dim]; - } /* end else */ - } /* end else */ - } /* end while */ - - /* Check if we are finished with the spans in the tree */ - if(curr_dim<0) { - /* We had better be done with I/O or bad things are going to happen... */ - break; - } /* end if */ - else { - /* Reset the span in the current dimension */ - iter->hyp.span[curr_dim]=curr_span; - - /* Walk back down the iterator positions, reseting them */ - while(curr_dim<fast_dim) { - assert(curr_span); - assert(curr_span->down); - assert(curr_span->down->head); - - /* Set the new span for this dimension */ - iter->hyp.span[curr_dim+1]=curr_span->down->head; - - /* Advance span down the tree */ - curr_span=curr_span->down->head; - - /* Reset the offset for the dim */ - off_arr[curr_dim+1]=curr_span->low; - coord_arr[curr_dim+1]=off_arr[curr_dim+1]+space->select.offset[curr_dim+1]; - - /* Increment current dimension */ - curr_dim++; - } /* end while */ - - /* Verify that the curr_span points to the fastest dim */ - assert(curr_span==iter->hyp.span[fast_dim]); - - /* Verify that the offset is correct for the fastest dim */ - assert(off_arr[fast_dim]==curr_span->low); - } /* end else */ - - /* Reset the buffer offset */ - for(i=0, loc_off=0; i<ndims; i++) - loc_off+=coord_arr[i]*slab[i]; - } /* end else */ - } /* end while */ - - /* Success! */ - ret_value=(user_ret==0 ? SUCCEED : user_ret); - -#ifdef LATER -done: -#endif /* LATER */ - FUNC_LEAVE (ret_value); -} /* end H5S_hyper_select_iterate_mem_gen() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S_hyper_select_iterate_mem_opt - PURPOSE - Iterate over the data points in a regular hyperslab selection, calling a - user's function for each element. - USAGE - herr_t H5S_hyper_select_iterate_mem_opt(buf, type_id, space, op, operator_data) - H5S_sel_iter_t *iter; IN/OUT: Selection iterator - void *buf; IN/OUT: Buffer containing elements to iterate over - hid_t type_id; IN: Datatype ID of BUF array. - H5S_t *space; IN: Dataspace object containing selection to iterate over - H5D_operator_t op; IN: Function pointer to the routine to be - called for each element in BUF iterated over. - void *op_data; IN/OUT: Pointer to any user-defined data associated - with the operation. - RETURNS - Returns the return value of the last operator if it was non-zero, or zero - if all elements were processed. Otherwise returns a negative value. - DESCRIPTION - Iterates over the selected elements in a memory buffer, calling the user's - callback function for each element. The selection in the dataspace is - modified so that any elements already iterated over are removed from the - selection if the iteration is interrupted (by the H5D_operator_t function - returning non-zero) in the "middle" of the iteration and may be re-started - by the user where it left off. - - NOTE: Until "subtracting" elements from a selection is implemented, - the selection is not modified. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5S_hyper_select_iterate_mem_opt(H5S_sel_iter_t UNUSED *iter, void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op, - void *op_data) -{ - H5S_hyper_dim_t *diminfo; /* Alias for dataspace's diminfo information */ - hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary hyperslab counts */ - hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary hyperslab blocks */ - hssize_t offset[H5O_LAYOUT_NDIMS]; /* Offset of element in dataspace */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Size of objects in buffer */ - size_t elem_size; /* Size of data element in buffer */ - hssize_t temp_off; /* Offset in a given dimension */ - uint8_t *loc; /* Current element location */ - int i; /* Counter */ - unsigned u; /* Counter */ - int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int temp_dim; /* Temporary rank holder */ - unsigned ndims; /* Rank of the dataspace */ - H5T_t *dt; /* Datatype structure */ - herr_t user_ret=0; /* User's return value */ - - FUNC_ENTER_NOINIT(H5S_hyper_select_iterate_mem_opt); - - /* Set some convienence values */ - ndims=space->extent.u.simple.rank; - fast_dim=ndims-1; - diminfo=space->select.sel_info.hslab.diminfo; - - /* Get the data element size */ - if (NULL==(dt=H5I_object(type_id))) - HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype"); - elem_size=H5T_get_size(dt); - - /* Elements in the fastest dimension are 'elem_size' */ - slab[ndims-1]=elem_size; - - /* If we have two or more dimensions, build the other dimension's element sizes */ - if(ndims>=2) { - /* Build the table of next-dimension down 'element' sizes */ - for(i=ndims-2; i>=0; i--) - slab[i]=slab[i+1]*space->extent.u.simple.size[i+1]; - } /* end if */ - - /* Build the tables of count & block sizes as well as the initial offset */ - for(u=0; u<ndims; u++) { - tmp_count[u]=diminfo[u].count; - tmp_block[u]=diminfo[u].block; - offset[u]=(diminfo[u].start+space->select.offset[u]); - } /* end for */ - - /* Initialize the starting location */ - for(loc=buf,u=0; u<ndims; u++) - loc+=offset[u]*slab[u]; - - /* Go iterate over the hyperslabs */ - while(user_ret==0) { - /* Iterate over the blocks in the fastest dimension */ - while(tmp_count[fast_dim]>0 && user_ret==0) { - - /* Iterate over the elements in the fastest dimension */ - while(tmp_block[fast_dim]>0 && user_ret==0) { - user_ret=(*op)(loc,type_id,(hsize_t)ndims,offset,op_data); - - /* Increment the buffer location */ - loc+=slab[fast_dim]; - - /* Increment the offset in the dataspace */ - offset[fast_dim]++; - - /* Decrement the sequence count */ - tmp_block[fast_dim]--; - } /* end while */ - - /* Reset the sequence count */ - tmp_block[fast_dim]=diminfo[fast_dim].block; - - /* Move the location to the next sequence to start */ - loc+=(diminfo[fast_dim].stride-diminfo[fast_dim].block)*slab[fast_dim]; - - /* Move the offset to the next sequence to start */ - offset[fast_dim]+=(diminfo[fast_dim].stride-diminfo[fast_dim].block); - - /* Decrement the block count */ - tmp_count[fast_dim]--; - } /* end while */ - - /* Check for getting out of iterator, we're done in the 1-D case */ - if(ndims==1) - goto done; /* Yes, an evil goto.. :-) -QAK */ - - /* Work on other dimensions if necessary */ - if(fast_dim>0 && user_ret==0) { - /* Reset the sequence and block counts */ - tmp_block[fast_dim]=diminfo[fast_dim].block; - tmp_count[fast_dim]=diminfo[fast_dim].count; - - /* Bubble up the decrement to the slower changing dimensions */ - temp_dim=fast_dim-1; - while(temp_dim>=0) { - /* Decrement the sequence count in this dimension */ - tmp_block[temp_dim]--; - - /* Check if we are still in the sequence */ - if(tmp_block[temp_dim]>0) - break; - - /* Reset the sequence count in this dimension */ - tmp_block[temp_dim]=diminfo[temp_dim].block; - - /* Decrement the block count */ - tmp_count[temp_dim]--; - - /* Check if we have more blocks left */ - if(tmp_count[temp_dim]>0) - break; - - /* Check for getting out of iterator */ - if(temp_dim==0) - goto done; /* Yes, an evil goto.. :-) -QAK */ - - /* Reset the block count in this dimension */ - tmp_count[temp_dim]=diminfo[temp_dim].count; - - /* Wrapped a dimension, go up to next dimension */ - temp_dim--; - } /* end while */ - } /* end if */ - - /* Re-compute buffer location & offset array */ - for(loc=buf,u=0; u<ndims; u++) { - temp_off=(diminfo[u].start+space->select.offset[u]) - +diminfo[u].stride*(diminfo[u].count-tmp_count[u]) - +(diminfo[u].block-tmp_block[u]); - loc+=temp_off*slab[u]; - offset[u]=temp_off; - } /* end for */ - } /* end while */ - -done: - FUNC_LEAVE (user_ret); -} /* end H5S_hyper_select_iterate_mem_opt() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S_hyper_select_iterate - PURPOSE - Iterate over a hyperslab selection, calling a user's function for each - element. - USAGE - herr_t H5S_hyper_select_iterate(buf, type_id, space, op, operator_data) - void *buf; IN/OUT: Buffer containing elements to iterate over - hid_t type_id; IN: Datatype ID of BUF array. - H5S_t *space; IN: Dataspace object containing selection to iterate over - H5D_operator_t op; IN: Function pointer to the routine to be - called for each element in BUF iterated over. - void *operator_data; IN/OUT: Pointer to any user-defined data - associated with the operation. - RETURNS - Returns the return value of the last operator if it was non-zero, or zero - if all elements were processed. Otherwise returns a negative value. - DESCRIPTION - Iterates over the selected elements in a memory buffer, calling the user's - callback function for each element. The selection in the dataspace is - modified so that any elements already iterated over are removed from the - selection if the iteration is interrupted (by the H5D_operator_t function - returning non-zero) in the "middle" of the iteration and may be re-started - by the user where it left off. - - NOTE: Until "subtracting" elements from a selection is implemented, - the selection is not modified. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -herr_t -H5S_hyper_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op, - void *operator_data) -{ - H5S_hyper_iter_info_t iter_info; /* Block of parameters to pass into recursive calls */ - H5S_sel_iter_t iter; /* selection iteration info*/ - size_t elmt_size; /* Datatype size */ - H5T_t *dt; /* Datatype structure */ - herr_t ret_value=FAIL; /* return value */ - - FUNC_ENTER_NOAPI(H5S_hyper_select_iterate, FAIL); - - assert(buf); - assert(space); - assert(op); - assert(H5I_DATATYPE == H5I_get_type(type_id)); - - /* Initialize iterator */ - HDmemset(&iter,0,sizeof(H5S_sel_iter_t)); - - /* Get the datatype size */ - if (NULL==(dt=H5I_object(type_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype"); - elmt_size=H5T_get_size(dt); - - /* Construct iterator for hyperslab selection */ - if (H5S_hyper_init(space, elmt_size, &iter)<0) - HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection information"); - - /* Check for the special case of just one H5Sselect_hyperslab call made */ - if(space->select.sel_info.hslab.diminfo!=NULL) { - /* Use optimized call to iterate over regular hyperslab */ - ret_value=H5S_hyper_select_iterate_mem_opt(&iter,buf,type_id,space,op,operator_data); - } - else { - /* Initialize parameter block for recursive calls */ - iter_info.dt=type_id; - iter_info.elem_size=elmt_size; - iter_info.space=space; - iter_info.iter=&iter; - iter_info.src=buf; - - /* Copy the location of the region in the file */ - iter_info.op=op; - iter_info.op_data=operator_data; - - /* Call the recursive iterator routine */ - ret_value=H5S_hyper_select_iterate_mem_gen(&iter_info); - } /* end else */ - - /* Release selection iterator */ - H5S_sel_iter_release(space,&iter); - -done: - FUNC_LEAVE (ret_value); -} /* H5S_hyper_select_iterate() */ - - -/*-------------------------------------------------------------------------- - NAME H5S_hyper_release PURPOSE Release hyperslab selection information for a dataspace @@ -6364,402 +2227,6 @@ done: /*-------------------------------------------------------------------------- NAME - H5S_hyper_select_fill_gen - PURPOSE - Fill a hyperslab selection in memory with a value - USAGE - herr_t H5S_hyper_select_fill_gen(fill,fill_size,space,buf) - const void *fill; IN: Pointer to fill value to use - size_t fill_size; IN: Size of elements in memory buffer & size of - fill value - H5S_t *space; IN: Dataspace describing memory buffer & - containing selection to use. - void *buf; IN/OUT: Memory buffer to fill selection in - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to fill elements in a memory buffer. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - The memory buffer elements are assumed to have the same datatype as the - fill value being placed into them. - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5S_hyper_select_fill_gen(const void *fill, size_t fill_size, const H5S_t *space, void *buf) -{ - H5S_hyper_span_info_t *spans=NULL; /* Pointer to copy of the span tree */ - H5S_hyper_span_info_t *tmp_spans; /* Temporary pointer to a span tree */ - H5S_hyper_span_t *span[H5O_LAYOUT_NDIMS]; /* Array of pointers to span nodes */ - H5S_hyper_span_t *curr_span; /* Current hyperslab span node */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Cumulative size of each dimension in bytes */ - hssize_t abs_arr[H5O_LAYOUT_NDIMS]; /* Absolute hyperslab span position */ - hssize_t *off_arr; /* Offset within the dataspace extent */ - hsize_t acc; /* Accumulator for computing cumulative sizes */ - int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int curr_dim; /* Current dimension being operated on */ - int ndims; /* Number of dimensions of dataset */ - hsize_t span_io; /* Number of elements in current span to actually process */ - hsize_t num_elem; /* Number of elements in the selection */ - uint8_t *loc; /* Current element location pointer */ - int i; /* Index variable */ - unsigned u; /* Index variable */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOINIT(H5S_hyper_select_fill_gen); - - /* Set the rank of the fastest changing dimension */ - ndims=space->extent.u.simple.rank; - fast_dim=(ndims-1); - - /* Set the pointer to the selection offset in the dataspace */ - off_arr=space->select.offset; - - /* Make a copy of the span tree to iterate over */ - spans=H5S_hyper_copy_span(space->select.sel_info.hslab.span_lst); - - /* Set the nelem & pstride values according to the element size */ - H5S_hyper_span_precompute(spans,fill_size); - - /* Build arrays of span heads & offsets in each dimension */ - for(u=0, tmp_spans=spans; u<space->extent.u.simple.rank; u++) { - /* Set the pointers to the initial span in each dimension */ - assert(tmp_spans); - assert(tmp_spans->head); - - /* Set the pointer to the first span in the list for this node */ - span[u] = tmp_spans->head; - - /* Set the initial offset to low bound of span */ - abs_arr[u]=span[u]->low; - - /* Get the pointer to the next level down */ - tmp_spans=tmp_spans->head->down; - } /* end for */ - - /* Compute sizes of "slab" in each dimension */ - for(i=fast_dim, acc=fill_size; i>=0; i--) { - slab[i]=acc; - acc*=space->extent.u.simple.size[i]; - } /* end for */ - - /* Set the offset of the first element iterated on */ - for(i=0, loc=buf; i<ndims; i++) - /* Compute the sequential element offset */ - loc+=(abs_arr[i]+off_arr[i])*slab[i]; - - /* Get the number of elements in selection */ - num_elem=space->select.num_elem; - - /* Get the pointer to the current span nodes */ - curr_span=span[fast_dim]; - - /* Go iterate over the hyperslabs */ - while(num_elem>0) { - /* Loop through the fastest dim's spans */ - while(curr_span!=NULL) { - /* Compute the number of elements to attempt in this span */ - span_io=(curr_span->high-curr_span->low)+1; - - /* Double check that things haven't gotten out of sync */ - assert(num_elem>0); - - /* Fill the elements in the current block */ - H5_CHECK_OVERFLOW(span_io,hsize_t,size_t); - H5V_array_fill(loc, fill, fill_size, (size_t)span_io); - - /* Increment the buffer offset */ - loc+=curr_span->pstride; - - /* Decrement the number of elements left */ - num_elem-=span_io; - - /* Advance span in fastest dimension */ - curr_span=curr_span->next; - } /* end while */ - - /* Check if there are more elements left */ - if(num_elem>0) { - /* Recursively advance to next offset (not necessarily span) in next dimension up */ - - /* Start at the fastest dim */ - curr_dim=fast_dim-1; - - /* Get the pointer to the correct dimension */ - curr_span=span[curr_dim]; - - /* Work back up through the dimensions */ - while(curr_dim>=0) { - /* Increment position in span */ - abs_arr[curr_dim]++; - - /* Check if we are still within the span */ - if(abs_arr[curr_dim]<=curr_span->high) { - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset the offset for the dim */ - abs_arr[curr_dim]=curr_span->low; - - break; - } /* end if */ - else { - /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ - curr_dim--; - - /* Reset the curr_span to the next dim */ - if(curr_dim>=0) - curr_span=span[curr_dim]; - } /* end else */ - } /* end else */ - } /* end while */ - - /* Reset the span in the current dimension */ - span[curr_dim]=curr_span; - - /* Walk back down the iterator positions, reseting them */ - while(curr_dim<fast_dim) { - assert(curr_span); - assert(curr_span->down); - assert(curr_span->down->head); - - /* Set the new span for this dimension */ - span[curr_dim+1]=curr_span->down->head; - - /* Advance span down the tree */ - curr_span=curr_span->down->head; - - /* Reset the offset for the dim */ - abs_arr[curr_dim+1]=curr_span->low; - - /* Increment current dimension */ - curr_dim++; - } /* end while */ - - /* Verify that the curr_span points to the fastest dim */ - assert(curr_span==span[fast_dim]); - - /* Verify that the offset is correct for the fastest dim */ - assert(abs_arr[fast_dim]==curr_span->low); - - /* Recompute offset in buffer */ - for(i=0, loc=buf; i<ndims; i++) - loc+=(abs_arr[i]+off_arr[i])*slab[i]; - } /* end if */ - } /* end while */ - -#ifdef LATER -done: -#endif /* LATER */ - /* Free the copy of the selections span tree */ - if(spans!=NULL) - H5S_hyper_free_span_info(spans); - - FUNC_LEAVE (ret_value); -} /* end H5S_hyper_select_fill_gen() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S_hyper_select_fill_opt - PURPOSE - Fill a hyperslab selection in memory with a value - USAGE - herr_t H5S_hyper_select_fill_opt(fill,fill_size,space,buf) - const void *fill; IN: Pointer to fill value to use - size_t fill_size; IN: Size of elements in memory buffer & size of - fill value - H5S_t *space; IN: Dataspace describing memory buffer & - containing selection to use. - void *buf; IN/OUT: Memory buffer to fill selection in - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to fill elements in a memory buffer. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - The memory buffer elements are assumed to have the same datatype as the - fill value being placed into them. - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5S_hyper_select_fill_opt(const void *fill, size_t fill_size, const H5S_t *space, void *buf) -{ - H5S_hyper_dim_t *diminfo; /* Alias for dataspace's diminfo information */ - hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary hyperslab counts */ - hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary hyperslab blocks */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Size of objects in buffer */ - hsize_t acc; /* Size accumulator */ - hsize_t num_elem; /* Number of elements in the selection */ - hsize_t fast_elem; /* Block size in the fastest dimension */ - hsize_t fast_stride; /* Stride in the fastest dimension */ - hssize_t temp_off; /* Offset in a given dimension */ - uint8_t *loc; /* Current element location */ - int i; /* Counter */ - unsigned u; /* Counter */ - int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int temp_dim; /* Temporary rank holder */ - unsigned ndims; /* Rank of the dataspace */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOINIT(H5S_hyper_select_fill_opt); - - /* Set some convienence values */ - ndims=space->extent.u.simple.rank; - fast_dim=ndims-1; - diminfo=space->select.sel_info.hslab.diminfo; - - /* Build the table of next-dimension down 'element' sizes */ - for(i=fast_dim, acc=fill_size; i>=0; i--) { - slab[i]=acc; - acc*=space->extent.u.simple.size[i]; - } /* end for */ - - /* Build the tables of count & block sizes as well as the initial starting location */ - for(u=0, loc=buf; u<ndims; u++) { - tmp_count[u]=diminfo[u].count; - tmp_block[u]=diminfo[u].block; - loc+=(diminfo[u].start+space->select.offset[u])*slab[u]; - } /* end for */ - - /* Get the number of elements in selection */ - num_elem=space->select.num_elem; - - /* Get the number of elements in the fastest dimension of the selection */ - fast_elem=tmp_block[fast_dim]; - fast_stride=diminfo[fast_dim].stride; - - /* Go iterate over the hyperslabs */ - while(num_elem>0) { - /* Iterate over the blocks in the fastest dimension */ - while(tmp_count[fast_dim]>0) { - /* Double check that things haven't gotten out of sync */ - assert(num_elem>0); - - /* Fill the elements in the current block */ - H5_CHECK_OVERFLOW(fast_elem,hsize_t,size_t); - H5V_array_fill(loc, fill, fill_size, (size_t)fast_elem); - - /* Advance the pointer in the memory buffer */ - loc+=(fast_stride*fill_size); - - /* Decrement the block count */ - tmp_count[fast_dim]--; - - /* Decrement the number of elements to process */ - num_elem-=fast_elem; - } /* end while */ - - /* Work on other dimensions if necessary */ - if(num_elem>0) { - /* Reset the sequence and block counts */ - tmp_count[fast_dim]=diminfo[fast_dim].count; - - /* Bubble up the decrement to the slower changing dimensions */ - temp_dim=fast_dim-1; - while(temp_dim>=0) { - /* Decrement the sequence count in this dimension */ - tmp_block[temp_dim]--; - - /* Check if we are still in the sequence */ - if(tmp_block[temp_dim]>0) - break; - - /* Reset the sequence count in this dimension */ - tmp_block[temp_dim]=diminfo[temp_dim].block; - - /* Decrement the block count */ - tmp_count[temp_dim]--; - - /* Check if we have more blocks left */ - if(tmp_count[temp_dim]>0) - break; - - /* Reset the block count in this dimension */ - tmp_count[temp_dim]=diminfo[temp_dim].count; - - /* Wrapped a dimension, go up to next dimension */ - temp_dim--; - } /* end while */ - - /* Re-compute buffer location */ - for(loc=buf,u=0; u<ndims; u++) { - temp_off=(diminfo[u].start+space->select.offset[u]) - +diminfo[u].stride*(diminfo[u].count-tmp_count[u]) - +(diminfo[u].block-tmp_block[u]); - loc+=temp_off*slab[u]; - } /* end for */ - } /* end if */ - } /* end while */ - -#ifdef LATER -done: -#endif /* LATER */ - FUNC_LEAVE (ret_value); -} /* end H5S_hyper_select_fill_opt() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S_hyper_select_fill - PURPOSE - Fill a hyperslab selection in memory with a value - USAGE - herr_t H5S_hyper_select_fill(fill,fill_size,space,buf) - const void *fill; IN: Pointer to fill value to use - size_t fill_size; IN: Size of elements in memory buffer & size of - fill value - H5S_t *space; IN: Dataspace describing memory buffer & - containing selection to use. - void *buf; IN/OUT: Memory buffer to fill selection in - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to fill elements in a memory buffer. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - The memory buffer elements are assumed to have the same datatype as the - fill value being placed into them. - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -herr_t -H5S_hyper_select_fill(const void *fill, size_t fill_size, const H5S_t *space, void *buf) -{ - herr_t ret_value=SUCCEED; /* return value */ - - FUNC_ENTER_NOAPI(H5S_hyper_select_fill, FAIL); - - /* Check args */ - assert(fill); - assert(fill_size>0); - assert(space); - assert(buf); - - /* Fill the selection in the memory buffer */ - - /* Check for the special case of just one H5Sselect_hyperslab call made */ - if(space->select.sel_info.hslab.diminfo!=NULL) - /* Use optimized call to fill regular hyperslab */ - ret_value=H5S_hyper_select_fill_opt(fill, fill_size, space, buf); - else - /* Call the general fill routine */ - ret_value=H5S_hyper_select_fill_gen(fill, fill_size, space, buf); - - FUNC_LEAVE (ret_value); -} /* H5S_hyper_select_fill() */ - - -/*-------------------------------------------------------------------------- - NAME H5S_hyper_recover_span PURPOSE Recover a generated span, if appropriate @@ -9263,3 +4730,1049 @@ done: FUNC_LEAVE (ret_value); } /* end H5Sselect_select() */ #endif /* NEW_HYPERSLAB_API */ /* Works */ + + +/*-------------------------------------------------------------------------- + NAME + H5S_hyper_select_get_seq_list_gen + PURPOSE + Create a list of offsets & lengths for a selection + USAGE + herr_t H5S_hyper_select_get_file_list_gen(space,iter,maxseq,nseq,off,len) + H5S_t *space; IN: Dataspace containing selection to use. + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + size_t elem_size; IN: Size of an element + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxbytes; IN: Maximum number of bytes to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + size_t *nbytes; OUT: Actual number of bytes in sequences generated + hsize_t *off; OUT: Array of offsets + size_t *len; OUT: Array of lengths + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +static herr_t +H5S_hyper_select_get_seq_list_gen(const H5S_t *space,H5S_sel_iter_t *iter, + size_t elem_size, size_t maxseq, size_t maxbytes, size_t *nseq, size_t *nbytes, + hsize_t *off, size_t *len) +{ + H5S_hyper_span_t *curr_span; /* Current hyperslab span node */ + H5S_hyper_span_t **ispan; /* Iterator's hyperslab span nodes */ + hsize_t slab[H5O_LAYOUT_NDIMS]; /* Cumulative size of each dimension in bytes */ + hsize_t acc; /* Accumulator for computing cumulative sizes */ + hsize_t loc_off; /* Element offset in the dataspace */ + hssize_t *abs_arr; /* Absolute hyperslab span position */ + hssize_t *off_arr; /* Offset within the dataspace extent */ + size_t span_size=0; /* Number of bytes in current span to actually process */ + size_t nelem; /* Number of elements left to process */ + size_t io_bytes_left; /* Number of bytes left to process */ + size_t start_io_bytes_left; /* Initial number of bytes left to process */ + size_t curr_seq=0; /* Number of sequence/offsets stored in the arrays */ + int ndims; /* Number of dimensions of dataset */ + int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ + int curr_dim; /* Current dimension being operated on */ + int i; /* Index variable */ + herr_t ret_value=SUCCEED; /* return value */ + + FUNC_ENTER_NOINIT (H5S_hyper_select_get_seq_list_gen); + + /* Check args */ + assert(space); + assert(iter); + assert(elem_size>0); + assert(maxseq>0); + assert(maxbytes>0); + assert(nseq); + assert(nbytes); + assert(off); + assert(len); + + /* "round" off the maxbytes allowed to a multiple of the element size */ + maxbytes=(maxbytes/elem_size)*elem_size; + + /* Set the rank of the fastest changing dimension */ + ndims=space->extent.u.simple.rank; + fast_dim=(ndims-1); + + /* Get the pointers to the current span info and span nodes */ + curr_span=iter->hyp.span[fast_dim]; + abs_arr=iter->hyp.off; + off_arr=space->select.offset; + ispan=iter->hyp.span; + + /* Set the amount of elements to perform I/O on, etc. */ + start_io_bytes_left=io_bytes_left=MIN(maxbytes,(iter->hyp.elmt_left*elem_size)); + nelem=io_bytes_left/elem_size; + + /* Compute the cumulative size of dataspace dimensions */ + for(i=fast_dim, acc=elem_size; i>=0; i--) { + slab[i]=acc; + acc*=space->extent.u.simple.size[i]; + } /* end for */ + + /* Set the offset of the first element iterated on */ + for(i=0, loc_off=0; i<ndims; i++) + /* Compute the sequential element offset */ + loc_off+=(abs_arr[i]+off_arr[i])*slab[i]; + + /* Range check against number of elements left in selection */ + assert(io_bytes_left<=(iter->hyp.elmt_left*elem_size)); + + /* Take care of any partial spans leftover from previous I/Os */ + if(abs_arr[fast_dim]!=curr_span->low) { + + /* Finish the span in the fastest changing dimension */ + + /* Compute the number of bytes to attempt in this span */ + H5_ASSIGN_OVERFLOW(span_size,((curr_span->high-abs_arr[fast_dim])+1)*elem_size,hsize_t,size_t); + + /* Check number of bytes against upper bounds allowed */ + if(span_size>io_bytes_left) + span_size=io_bytes_left; + + /* Add the partial span to the list of sequences */ + off[curr_seq]=loc_off; + len[curr_seq]=span_size; + + /* Increment sequence count */ + curr_seq++; + + /* Decrement I/O left to perform */ + io_bytes_left-=span_size; + + /* Advance the hyperslab iterator */ + /* Check if we are done */ + if(io_bytes_left>0) { + /* Move to next span in fastest changing dimension */ + curr_span=curr_span->next; + + if(curr_span!=NULL) { + /* Move location offset of destination */ + loc_off+=(curr_span->low-abs_arr[fast_dim])*elem_size; + + /* Move iterator for fastest changing dimension */ + abs_arr[fast_dim]=curr_span->low; + } /* end if */ + } /* end if */ + else { + abs_arr[fast_dim]+=span_size/elem_size; + + /* Check if we are still within the span */ + if(abs_arr[fast_dim]<=curr_span->high) { + iter->hyp.span[fast_dim]=curr_span; + + goto partial_done; /* finished with partial span */ + } /* end if */ + /* If we walked off that span, advance to the next span */ + else { + /* Advance span in this dimension */ + curr_span=curr_span->next; + + /* Check if we have a valid span in this dimension still */ + if(curr_span!=NULL) { + /* Reset absolute position */ + abs_arr[fast_dim]=curr_span->low; + iter->hyp.span[fast_dim]=curr_span; + + goto partial_done; /* finished with partial span */ + } /* end if */ + } /* end else */ + } /* end else */ + + /* Adjust iterator pointers */ + + if(curr_span==NULL) { +/* Same as code in main loop */ + /* Start at the next fastest dim */ + curr_dim=fast_dim-1; + + /* Work back up through the dimensions */ + while(curr_dim>=0) { + /* Reset the current span */ + curr_span=iter->hyp.span[curr_dim]; + + /* Increment absolute position */ + abs_arr[curr_dim]++; + + /* Check if we are still within the span */ + if(abs_arr[curr_dim]<=curr_span->high) { + break; + } /* end if */ + /* If we walked off that span, advance to the next span */ + else { + /* Advance span in this dimension */ + curr_span=curr_span->next; + + /* Check if we have a valid span in this dimension still */ + if(curr_span!=NULL) { + /* Reset the span in the current dimension */ + ispan[curr_dim]=curr_span; + + /* Reset absolute position */ + abs_arr[curr_dim]=curr_span->low; + + break; + } /* end if */ + else { + /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ + curr_dim--; + } /* end else */ + } /* end else */ + } /* end while */ + + /* Check if we are finished with the spans in the tree */ + if(curr_dim<0) { + /* We had better be done with I/O or bad things are going to happen... */ + assert(io_bytes_left==0); + + goto partial_done; /* finished with partial span */ + } /* end if */ + else { + /* Walk back down the iterator positions, reseting them */ + while(curr_dim<fast_dim) { + assert(curr_span); + assert(curr_span->down); + assert(curr_span->down->head); + + /* Increment current dimension */ + curr_dim++; + + /* Set the new span_info & span for this dimension */ + iter->hyp.span[curr_dim]=curr_span->down->head; + + /* Advance span down the tree */ + curr_span=curr_span->down->head; + + /* Reset the absolute offset for the dim */ + abs_arr[curr_dim]=curr_span->low; + } /* end while */ + + /* Verify that the curr_span points to the fastest dim */ + assert(curr_span==iter->hyp.span[fast_dim]); + } /* end else */ + + /* Reset the buffer offset */ + for(i=0, loc_off=0; i<ndims; i++) + loc_off+=(abs_arr[i]+off_arr[i])*slab[i]; + } /* end if */ + } /* end if */ + +partial_done: /* Yes, goto's are evil, so sue me... :-) */ + + /* Perform the I/O on the elements, based on the position of the iterator */ + while(io_bytes_left>0 && curr_seq<maxseq) { + /* Adjust location offset of destination to compensate for initial increment below */ + loc_off-=curr_span->pstride; + + /* Loop over all the spans in the fastest changing dimension */ + while(curr_span!=NULL) { + /* Move location offset of destination */ + loc_off+=curr_span->pstride; + + /* Compute the number of elements to attempt in this span */ + H5_ASSIGN_OVERFLOW(span_size,curr_span->nelem,hsize_t,size_t); + + /* Check number of elements against upper bounds allowed */ + if(span_size>=io_bytes_left) { + /* Trim the number of bytes to output */ + span_size=io_bytes_left; + io_bytes_left=0; + +/* COMMON */ + /* Store the I/O information for the span */ + off[curr_seq]=loc_off; + len[curr_seq]=span_size; + + /* Increment the number of sequences in arrays */ + curr_seq++; + + /* If the sequence & offset arrays are full, do what? */ + if(curr_seq>=maxseq) { + /* Break out now, we are finished with sequences */ + break; + + } /* end else */ +/* end COMMON */ + + /* Break out now, we are finished with I/O */ + break; + } /* end if */ + else { + /* Decrement I/O left to perform */ + io_bytes_left-=span_size; + +/* COMMON */ + /* Store the I/O information for the span */ + off[curr_seq]=loc_off; + len[curr_seq]=span_size; + + /* Increment the number of sequences in arrays */ + curr_seq++; + + /* If the sequence & offset arrays are full, do what? */ + if(curr_seq>=maxseq) { + /* Break out now, we are finished with sequences */ + break; + } /* end else */ +/* end COMMON */ + } /* end else */ + + /* Move to next span in fastest changing dimension */ + curr_span=curr_span->next; + } /* end while */ + + /* Check if we are done */ + if(io_bytes_left==0 || curr_seq>=maxseq) { + abs_arr[fast_dim]=curr_span->low+(span_size/elem_size); + + /* Check if we are still within the span */ + if(abs_arr[fast_dim]<=curr_span->high) { + iter->hyp.span[fast_dim]=curr_span; + break; + } /* end if */ + /* If we walked off that span, advance to the next span */ + else { + /* Advance span in this dimension */ + curr_span=curr_span->next; + + /* Check if we have a valid span in this dimension still */ + if(curr_span!=NULL) { + /* Reset absolute position */ + abs_arr[fast_dim]=curr_span->low; + iter->hyp.span[fast_dim]=curr_span; + break; + } /* end if */ + } /* end else */ + } /* end if */ + + /* Adjust iterator pointers */ + + /* Start at the next fastest dim */ + curr_dim=fast_dim-1; + + /* Work back up through the dimensions */ + while(curr_dim>=0) { + /* Reset the current span */ + curr_span=iter->hyp.span[curr_dim]; + + /* Increment absolute position */ + abs_arr[curr_dim]++; + + /* Check if we are still within the span */ + if(abs_arr[curr_dim]<=curr_span->high) { + break; + } /* end if */ + /* If we walked off that span, advance to the next span */ + else { + /* Advance span in this dimension */ + curr_span=curr_span->next; + + /* Check if we have a valid span in this dimension still */ + if(curr_span!=NULL) { + /* Reset the span in the current dimension */ + ispan[curr_dim]=curr_span; + + /* Reset absolute position */ + abs_arr[curr_dim]=curr_span->low; + + break; + } /* end if */ + else { + /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ + curr_dim--; + } /* end else */ + } /* end else */ + } /* end while */ + + /* Check if we are finished with the spans in the tree */ + if(curr_dim<0) { + /* We had better be done with I/O or bad things are going to happen... */ + assert(io_bytes_left==0); + break; + } /* end if */ + else { + /* Walk back down the iterator positions, reseting them */ + while(curr_dim<fast_dim) { + assert(curr_span); + assert(curr_span->down); + assert(curr_span->down->head); + + /* Increment current dimension to the next dimension down */ + curr_dim++; + + /* Set the new span for the next dimension down */ + iter->hyp.span[curr_dim]=curr_span->down->head; + + /* Advance span down the tree */ + curr_span=curr_span->down->head; + + /* Reset the absolute offset for the dim */ + abs_arr[curr_dim]=curr_span->low; + } /* end while */ + + /* Verify that the curr_span points to the fastest dim */ + assert(curr_span==iter->hyp.span[fast_dim]); + } /* end else */ + + /* Reset the buffer offset */ + for(i=0, loc_off=0; i<ndims; i++) + loc_off+=(abs_arr[i]+off_arr[i])*slab[i]; + } /* end while */ + + /* Decrement number of elements left in iterator */ + iter->hyp.elmt_left-=(nelem-(io_bytes_left/elem_size)); + + /* Set the number of sequences generated */ + *nseq=curr_seq; + + /* Set the number of bytes used */ + *nbytes=(start_io_bytes_left-io_bytes_left); + +#ifdef LATER +done: +#endif /* LATER */ + FUNC_LEAVE (ret_value); +} /* end H5S_hyper_select_get_seq_list_gen() */ + + +/*-------------------------------------------------------------------------- + NAME + H5S_hyper_select_get_seq_list_opt + PURPOSE + Create a list of offsets & lengths for a selection + USAGE + herr_t H5S_hyper_select_get_file_list_opt(space,iter,maxseq,nseq,off,len) + H5S_t *space; IN: Dataspace containing selection to use. + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + size_t elem_size; IN: Size of an element + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxbytes; IN: Maximum number of bytes to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + size_t *nbytes; OUT: Actual number of bytes in sequences generated + hsize_t *off; OUT: Array of offsets + size_t *len; OUT: Array of lengths + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +static herr_t +H5S_hyper_select_get_seq_list_opt(const H5S_t *space,H5S_sel_iter_t *iter, + size_t elmt_size, size_t maxseq, size_t maxbytes, size_t *nseq, size_t *nbytes, + hsize_t *off, size_t *len) +{ + hsize_t mem_size[H5O_LAYOUT_NDIMS]; /* Size of the source buffer */ + hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */ + hssize_t *sel_off; /* Selection offset in dataspace */ + hssize_t offset[H5O_LAYOUT_NDIMS]; /* Coordinate offset in dataspace */ + hsize_t tmp_count[H5O_LAYOUT_NDIMS];/* Temporary block count */ + hsize_t tmp_block[H5O_LAYOUT_NDIMS];/* Temporary block offset */ + hssize_t wrap[H5O_LAYOUT_NDIMS]; /* Bytes to wrap around at the end of a row */ + hsize_t skip[H5O_LAYOUT_NDIMS]; /* Bytes to skip between blocks */ + const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ + hssize_t fast_dim_start, /* Local copies of fastest changing dimension info */ + fast_dim_offset; + hsize_t fast_dim_stride, /* Local copies of fastest changing dimension info */ + fast_dim_block; + size_t fast_dim_buf_off; /* Local copy of amount to move fastest dimension buffer offset */ + size_t fast_dim_count; /* Number of blocks left in fastest changing dimension */ + size_t tot_blk_count; /* Total number of blocks left to output */ + size_t act_blk_count; /* Actual number of blocks to output */ + size_t total_rows; /* Total number of entire rows to output */ + size_t curr_rows; /* Current number of entire rows to output */ + int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ + int temp_dim; /* Temporary rank holder */ + int ndims; /* Number of dimensions of dataset */ + hsize_t acc; /* Accumulator */ + hsize_t loc; /* Coordinate offset */ + int i; /* Local index variable */ + size_t curr_seq=0; /* Current sequence being operated on */ + size_t actual_elem; /* The actual number of elements to count */ + size_t actual_bytes;/* The actual number of bytes to copy */ + size_t nelmts; /* Starting number of elements */ + size_t io_left; /* The number of elements left in I/O operation */ + size_t start_io_left; /* The initial number of elements left in I/O operation */ +#ifndef NO_DUFFS_DEVICE + size_t duffs_index; /* Counting index for Duff's device */ +#endif /* NO_DUFFS_DEVICE */ + herr_t ret_value=SUCCEED; /* return value */ + + FUNC_ENTER_NOINIT (H5S_hyper_select_get_seq_list_opt); + + /* Check args */ + assert(space); + assert(iter); + assert(elmt_size>0); + assert(maxseq>0); + assert(maxbytes>0); + assert(nseq); + assert(nbytes); + assert(off); + assert(len); + + /* Check if this is a "flattened" regular hyperslab selection */ + if(iter->hyp.iter_rank!=0 && iter->hyp.iter_rank<space->extent.u.simple.rank) { + /* Set the aliases for a few important dimension ranks */ + ndims=iter->hyp.iter_rank; + fast_dim=ndims-1; + + /* Set the local copy of the diminfo pointer */ + tdiminfo=iter->hyp.diminfo; + + /* Set the local copy of the selection offset */ + sel_off=iter->hyp.sel_off; + + /* Set up the size of the memory space */ + HDmemcpy(mem_size, iter->hyp.size, ndims*sizeof(hsize_t)); + } /* end if */ + else { + /* Set the aliases for a few important dimension ranks */ + ndims=space->extent.u.simple.rank; + fast_dim=ndims-1; + + /* Set the local copy of the diminfo pointer */ + tdiminfo=space->select.sel_info.hslab.diminfo; + + /* Set the local copy of the selection offset */ + sel_off=space->select.offset; + + /* Set up the size of the memory space */ + HDmemcpy(mem_size, space->extent.u.simple.size, ndims*sizeof(hsize_t)); + } /* end else */ + mem_size[ndims]=elmt_size; + + /* initialize row sizes for each dimension */ + for(i=(ndims-1),acc=1; i>=0; i--) { + slab[i]=acc*elmt_size; + acc*=mem_size[i]; + } /* end for */ + + /* Get the number of elements left in the selection */ + H5_ASSIGN_OVERFLOW(io_left,iter->hyp.elmt_left,hsize_t,size_t); + + /* Calculate the number of elements to sequence through */ + start_io_left=io_left=MIN(io_left,(maxbytes/elmt_size)); + + /* Check if we stopped in the middle of a sequence of elements */ + if((iter->hyp.off[fast_dim]-tdiminfo[fast_dim].start)%tdiminfo[fast_dim].stride!=0 || + ((iter->hyp.off[fast_dim]!=tdiminfo[fast_dim].start) && tdiminfo[fast_dim].stride==1)) { + size_t leftover; /* The number of elements left over from the last sequence */ + + /* Calculate the number of elements left in the sequence */ + if(tdiminfo[fast_dim].stride==1) + leftover=tdiminfo[fast_dim].block-(iter->hyp.off[fast_dim]-tdiminfo[fast_dim].start); + else + leftover=tdiminfo[fast_dim].block-((iter->hyp.off[fast_dim]-tdiminfo[fast_dim].start)%tdiminfo[fast_dim].stride); + + /* Make certain that we don't write too many */ + actual_elem=MIN(leftover,io_left); + + /* Compute the initial buffer offset */ + for(i=0,loc=0; i<ndims; i++) + loc+=(iter->hyp.off[i]+sel_off[i])*slab[i]; + + /* Add a new sequence */ + off[curr_seq]=loc; + H5_ASSIGN_OVERFLOW(len[curr_seq],actual_elem*elmt_size,hsize_t,size_t); + + /* Increment sequence count */ + curr_seq++; + + /* Decrement the number of elements left */ + io_left -= actual_elem; + + /* Advance the hyperslab iterator */ + + /* If we had enough room to count the rest of the sequence + * in the fastest changing dimension, move the iterator offset to + * the beginning of the next block to write. Otherwise, just advance + * the iterator in the fastest changing dimension. + */ + if(actual_elem==leftover) { + /* Move iterator offset to beginning of next sequence in the fastest changing dimension */ + H5S_hyper_iter_next(space,iter); + } /* end if */ + else { + iter->hyp.off[fast_dim]+=actual_elem; /* whole sequence not written out, just advance fastest dimension offset */ + } /* end else */ + + /* Decrement the number of elements left in selection */ + iter->hyp.elmt_left-=actual_elem; + } /* end if */ + + /* Now that we've cleared the "remainder" of the previous fastest dimension + * sequence, we must be at the beginning of a sequence, so use the fancy + * algorithm to compute the offsets and run through as many as possible, + * until the buffer fills up. + */ + if(io_left>0 && curr_seq<maxseq) { /* Just in case the "remainder" above filled the buffer */ + /* Keep the number of elements we started with */ + nelmts=io_left; + + /* Compute the arrays to perform I/O on */ + /* Copy the location of the point to get */ + HDmemcpy(offset, iter->hyp.off,ndims*sizeof(hssize_t)); + + /* Add in the selection offset */ + for(i=0; i<ndims; i++) + offset[i] += sel_off[i]; + + /* Compute the current "counts" for this location */ + for(i=0; i<ndims; i++) { + if(tdiminfo[i].stride==1) { + tmp_count[i] = 0; + tmp_block[i] = iter->hyp.off[i]-tdiminfo[i].start; + } /* end if */ + else { + tmp_count[i] = (iter->hyp.off[i]-tdiminfo[i].start)/tdiminfo[i].stride; + tmp_block[i] = (iter->hyp.off[i]-tdiminfo[i].start)%tdiminfo[i].stride; + } /* end else */ + } /* end for */ + + /* Compute the initial buffer offset */ + for(i=0,loc=0; i<ndims; i++) + loc+=offset[i]*slab[i]; + + /* Set the number of elements to write each time */ + H5_ASSIGN_OVERFLOW(actual_elem,tdiminfo[fast_dim].block,hsize_t,size_t); + + /* Set the number of actual bytes */ + actual_bytes=actual_elem*elmt_size; + + /* Set local copies of information for the fastest changing dimension */ + fast_dim_start=tdiminfo[fast_dim].start; + fast_dim_stride=tdiminfo[fast_dim].stride; + fast_dim_block=tdiminfo[fast_dim].block; + H5_ASSIGN_OVERFLOW(fast_dim_buf_off,slab[fast_dim]*fast_dim_stride,hsize_t,size_t); + fast_dim_offset=fast_dim_start+sel_off[fast_dim]; + + /* Compute the number of blocks which would fit into the buffer */ + tot_blk_count=io_left/fast_dim_block; + + /* Don't go over the maximum number of sequences allowed */ + tot_blk_count=MIN(tot_blk_count,(maxseq-curr_seq)); + + /* Compute the amount to wrap at the end of each row */ + for(i=0; i<ndims; i++) + wrap[i]=(mem_size[i]-(tdiminfo[i].stride*tdiminfo[i].count))*slab[i]; + + /* Compute the amount to skip between blocks */ + for(i=0; i<ndims; i++) + skip[i]=(tdiminfo[i].stride-tdiminfo[i].block)*slab[i]; + + /* Check if there is a partial row left (with full blocks) */ + if(tmp_count[fast_dim]>0) { + /* Get number of blocks in fastest dimension */ + H5_ASSIGN_OVERFLOW(fast_dim_count,tdiminfo[fast_dim].count-tmp_count[fast_dim],hsize_t,size_t); + + /* Make certain this entire row will fit into buffer */ + fast_dim_count=MIN(fast_dim_count,tot_blk_count); + + /* Number of blocks to sequence over */ + act_blk_count=fast_dim_count; + + /* Loop over all the blocks in the fastest changing dimension */ + while(fast_dim_count>0) { + /* Store the sequence information */ + off[curr_seq]=loc; + len[curr_seq]=actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc+=fast_dim_buf_off; + + /* Decrement number of blocks */ + fast_dim_count--; + } /* end while */ + + /* Decrement number of elements left */ + io_left -= actual_elem*act_blk_count; + + /* Decrement number of blocks left */ + tot_blk_count -= act_blk_count; + + /* Increment information to reflect block just processed */ + tmp_count[fast_dim]+=act_blk_count; + + /* Check if we finished the entire row of blocks */ + if(tmp_count[fast_dim]>=tdiminfo[fast_dim].count) { + /* Increment offset in destination buffer */ + loc += wrap[fast_dim]; + + /* Increment information to reflect block just processed */ + offset[fast_dim]=fast_dim_offset; /* reset the offset in the fastest dimension */ + tmp_count[fast_dim]=0; + + /* Increment the offset and count for the other dimensions */ + temp_dim=fast_dim-1; + while(temp_dim>=0) { + /* Move to the next row in the curent dimension */ + offset[temp_dim]++; + tmp_block[temp_dim]++; + + /* If this block is still in the range of blocks to output for the dimension, break out of loop */ + if(tmp_block[temp_dim]<tdiminfo[temp_dim].block) + break; + else { + /* Move to the next block in the current dimension */ + offset[temp_dim]+=(tdiminfo[temp_dim].stride-tdiminfo[temp_dim].block); + loc += skip[temp_dim]; + tmp_block[temp_dim]=0; + tmp_count[temp_dim]++; + + /* If this block is still in the range of blocks to output for the dimension, break out of loop */ + if(tmp_count[temp_dim]<tdiminfo[temp_dim].count) + break; + else { + offset[temp_dim]=tdiminfo[temp_dim].start+sel_off[temp_dim]; + loc += wrap[temp_dim]; + tmp_count[temp_dim]=0; /* reset back to the beginning of the line */ + tmp_block[temp_dim]=0; + } /* end else */ + } /* end else */ + + /* Decrement dimension count */ + temp_dim--; + } /* end while */ + } /* end if */ + else { + /* Update the offset in the fastest dimension */ + offset[fast_dim]+=(fast_dim_stride*act_blk_count); + } /* end else */ + } /* end if */ + + /* Compute the number of entire rows to read in */ + curr_rows=total_rows=tot_blk_count/tdiminfo[fast_dim].count; + + /* Reset copy of number of blocks in fastest dimension */ + H5_ASSIGN_OVERFLOW(fast_dim_count,tdiminfo[fast_dim].count,hsize_t,size_t); + + /* Read in data until an entire sequence can't be written out any longer */ + while(curr_rows>0) { +#ifdef NO_DUFFS_DEVICE + /* Loop over all the blocks in the fastest changing dimension */ + while(fast_dim_count>0) { + /* Store the sequence information */ + off[curr_seq]=loc; + len[curr_seq]=actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc+=fast_dim_buf_off; + + /* Decrement number of blocks */ + fast_dim_count--; + } /* end while */ +#else /* NO_DUFFS_DEVICE */ + duffs_index = (fast_dim_count + 7) / 8; + switch (fast_dim_count % 8) { + case 0: + do + { + /* Store the sequence information */ + off[curr_seq]=loc; + len[curr_seq]=actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc+=fast_dim_buf_off; + + case 7: + /* Store the sequence information */ + off[curr_seq]=loc; + len[curr_seq]=actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc+=fast_dim_buf_off; + + case 6: + /* Store the sequence information */ + off[curr_seq]=loc; + len[curr_seq]=actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc+=fast_dim_buf_off; + + case 5: + /* Store the sequence information */ + off[curr_seq]=loc; + len[curr_seq]=actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc+=fast_dim_buf_off; + + case 4: + /* Store the sequence information */ + off[curr_seq]=loc; + len[curr_seq]=actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc+=fast_dim_buf_off; + + case 3: + /* Store the sequence information */ + off[curr_seq]=loc; + len[curr_seq]=actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc+=fast_dim_buf_off; + + case 2: + /* Store the sequence information */ + off[curr_seq]=loc; + len[curr_seq]=actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc+=fast_dim_buf_off; + + case 1: + /* Store the sequence information */ + off[curr_seq]=loc; + len[curr_seq]=actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc+=fast_dim_buf_off; + + } while (--duffs_index > 0); + } /* end switch */ +#endif /* NO_DUFFS_DEVICE */ + + /* Increment offset in destination buffer */ + loc += wrap[fast_dim]; + + /* Increment the offset and count for the other dimensions */ + temp_dim=fast_dim-1; + while(temp_dim>=0) { + /* Move to the next row in the curent dimension */ + offset[temp_dim]++; + tmp_block[temp_dim]++; + + /* If this block is still in the range of blocks to output for the dimension, break out of loop */ + if(tmp_block[temp_dim]<tdiminfo[temp_dim].block) + break; + else { + /* Move to the next block in the current dimension */ + offset[temp_dim]+=(tdiminfo[temp_dim].stride-tdiminfo[temp_dim].block); + loc += skip[temp_dim]; + tmp_block[temp_dim]=0; + tmp_count[temp_dim]++; + + /* If this block is still in the range of blocks to output for the dimension, break out of loop */ + if(tmp_count[temp_dim]<tdiminfo[temp_dim].count) + break; + else { + offset[temp_dim]=tdiminfo[temp_dim].start+sel_off[temp_dim]; + loc += wrap[temp_dim]; + tmp_count[temp_dim]=0; /* reset back to the beginning of the line */ + tmp_block[temp_dim]=0; + } /* end else */ + } /* end else */ + + /* Decrement dimension count */ + temp_dim--; + } /* end while */ + + /* Decrement the number of rows left */ + curr_rows--; + } /* end while */ + + /* Adjust the number of blocks & elements left to transfer */ + + /* Decrement number of elements left */ + io_left -= actual_elem*(total_rows*tdiminfo[fast_dim].count); + + /* Decrement number of blocks left */ + tot_blk_count -= (total_rows*tdiminfo[fast_dim].count); + + /* Read in partial row of blocks */ + if(io_left>0 && curr_seq<maxseq) { + /* Get remaining number of blocks left to output */ + fast_dim_count=tot_blk_count; + + /* Loop over all the blocks in the fastest changing dimension */ + while(fast_dim_count>0) { + /* Store the sequence information */ + off[curr_seq]=loc; + len[curr_seq]=actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc+=fast_dim_buf_off; + + /* Decrement number of blocks */ + fast_dim_count--; + } /* end while */ + + /* Decrement number of elements left */ + io_left -= actual_elem*tot_blk_count; + + /* Increment information to reflect block just processed */ + offset[fast_dim]+=(fast_dim_stride*tot_blk_count); /* move the offset in the fastest dimension */ + + /* Handle any leftover, partial blocks in this row */ + if(io_left>0 && curr_seq<maxseq) { + actual_elem=io_left; + actual_bytes=actual_elem*elmt_size; + + /* Store the sequence information */ + off[curr_seq]=loc; + len[curr_seq]=actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Decrement the number of elements left */ + io_left -= actual_elem; + + /* Increment buffer correctly */ + offset[fast_dim]+=actual_elem; + } /* end if */ + + /* don't bother checking slower dimensions */ + assert(io_left==0 || curr_seq==maxseq); + } /* end if */ + + + /* Update the iterator */ + + /* Subtract out the selection offset */ + for(i=0; i<ndims; i++) + offset[i] -= sel_off[i]; + + /* Update the iterator with the location we stopped */ + HDmemcpy(iter->hyp.off, offset, ndims*sizeof(hssize_t)); + + /* Decrement the number of elements left in selection */ + iter->hyp.elmt_left-=(nelmts-io_left); + } /* end if */ + + /* Set the number of sequences generated */ + *nseq=curr_seq; + + /* Set the number of bytes used */ + *nbytes=(start_io_left-io_left)*elmt_size; + +#ifdef LATER +done: +#endif /* LATER */ + FUNC_LEAVE (ret_value); +} /* end H5S_hyper_select_get_seq_list_opt() */ + + +/*-------------------------------------------------------------------------- + NAME + H5S_hyper_select_get_seq_list + PURPOSE + Create a list of offsets & lengths for a selection + USAGE + herr_t H5S_hyper_select_get_seq_list(flags,space,iter,elem_size,maxseq,maxbytes,nseq,nbytes,off,len) + unsigned flags; IN: Flags for extra information about operation + H5S_t *space; IN: Dataspace containing selection to use. + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + size_t elem_size; IN: Size of an element + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxbytes; IN: Maximum number of bytes to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + size_t *nbytes; OUT: Actual number of bytes in sequences generated + hsize_t *off; OUT: Array of offsets + size_t *len; OUT: Array of lengths + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +herr_t +H5S_hyper_select_get_seq_list(unsigned UNUSED flags, const H5S_t *space,H5S_sel_iter_t *iter, + size_t elem_size, size_t maxseq, size_t maxbytes, size_t *nseq, size_t *nbytes, + hsize_t *off, size_t *len) +{ + herr_t ret_value=FAIL; /* return value */ + + FUNC_ENTER_NOAPI (H5S_hyper_select_get_seq_list, FAIL); + + /* Check args */ + assert(space); + assert(iter); + assert(elem_size>0); + assert(maxseq>0); + assert(maxbytes>0); + assert(nseq); + assert(nbytes); + assert(off); + assert(len); + + /* Check for the special case of just one H5Sselect_hyperslab call made */ + if(space->select.sel_info.hslab.diminfo!=NULL) + /* Use optimized call to generate sequence list */ + ret_value=H5S_hyper_select_get_seq_list_opt(space,iter,elem_size,maxseq,maxbytes,nseq,nbytes,off,len); + else + /* Call the general sequence generator routine */ + ret_value=H5S_hyper_select_get_seq_list_gen(space,iter,elem_size,maxseq,maxbytes,nseq,nbytes,off,len); + +#ifdef LATER +done: +#endif /* LATER */ + FUNC_LEAVE (ret_value); +} /* end H5S_hyper_select_get_seq_list() */ + diff --git a/src/H5Spkg.h b/src/H5Spkg.h index 1ab7dd6..d31d894 100644 --- a/src/H5Spkg.h +++ b/src/H5Spkg.h @@ -72,12 +72,12 @@ struct H5S_hyper_span_info_t { }; /* Information about one dimension in a hyperslab selection */ -typedef struct { +struct H5S_hyper_dim_t { hssize_t start; hsize_t stride; hsize_t count; hsize_t block; -} H5S_hyper_dim_t; +}; /* Information about new-style hyperslab selection */ typedef struct { @@ -117,10 +117,12 @@ struct H5S_t { __DLL__ herr_t H5S_close_simple(H5S_simple_t *simple); __DLL__ herr_t H5S_release_simple(H5S_simple_t *simple); __DLL__ herr_t H5S_extent_copy(H5S_extent_t *dst, const H5S_extent_t *src); -__DLL__ herr_t H5S_register(H5S_sel_type cls, const H5S_fconv_t *fconv, - const H5S_mconv_t *mconv); /* Point select functions */ +__DLL__ herr_t H5S_point_init (const H5S_t *space, size_t elmt_size, + H5S_sel_iter_t *iter); +__DLL__ hsize_t H5S_point_favail (const H5S_t *space, const H5S_sel_iter_t *iter, + hsize_t max); __DLL__ herr_t H5S_point_add(H5S_t *space, H5S_seloper_t op, size_t num_elem, const hssize_t **coord); __DLL__ herr_t H5S_point_release(H5S_t *space); @@ -136,33 +138,29 @@ __DLL__ htri_t H5S_point_select_single(const H5S_t *space); __DLL__ htri_t H5S_point_select_regular(const H5S_t *space); __DLL__ herr_t H5S_select_elements (H5S_t *space, H5S_seloper_t op, size_t num_elem, const hssize_t **coord); -__DLL__ herr_t H5S_point_select_iterate(void *buf, hid_t type_id, H5S_t *space, - H5D_operator_t op, void *operator_data); -__DLL__ herr_t H5S_point_select_fill(const void *fill, size_t fill_size, - const H5S_t *space, void *buf); +__DLL__ herr_t H5S_point_select_get_seq_list(unsigned flags, const H5S_t *space,H5S_sel_iter_t *iter, + size_t elem_size, size_t maxseq, size_t maxbytes, + size_t *nseq, size_t *nbytes, hsize_t *off, size_t *len); /* "All" select functions */ +__DLL__ herr_t H5S_all_init (const H5S_t *space, size_t elmt_size, + H5S_sel_iter_t *iter); +__DLL__ hsize_t H5S_all_favail (const H5S_t *space, const H5S_sel_iter_t *iter, + hsize_t max); __DLL__ herr_t H5S_all_release(H5S_t *space); __DLL__ hsize_t H5S_all_npoints(const H5S_t *space); __DLL__ herr_t H5S_all_select_serialize(const H5S_t *space, uint8_t *buf); __DLL__ herr_t H5S_all_select_deserialize(H5S_t *space, const uint8_t *buf); __DLL__ herr_t H5S_all_bounds(H5S_t *space, hsize_t *start, hsize_t *end); -__DLL__ herr_t H5S_all_read(H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, const H5S_t *mem_space, - hid_t dxpl_id, void *buf/*out*/); -__DLL__ herr_t H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, const H5S_t *mem_space, - hid_t dxpl_id, const void *buf); -__DLL__ herr_t H5S_all_select_iterate(void *buf, hid_t type_id, H5S_t *space, - H5D_operator_t op, void *operator_data); -__DLL__ herr_t H5S_all_select_fill(const void *fill, size_t fill_size, - const H5S_t *space, void *buf); -__DLL__ htri_t H5S_all_opt_possible(const H5S_t *mem_space, - const H5S_t *file_space, const unsigned flags); +__DLL__ herr_t H5S_all_select_get_seq_list(unsigned flags, const H5S_t *space,H5S_sel_iter_t *iter, + size_t elem_size, size_t maxseq, size_t maxbytes, + size_t *nseq, size_t *nbytes, hsize_t *off, size_t *len); /* Hyperslab selection functions */ +__DLL__ herr_t H5S_hyper_init (const H5S_t *space, size_t elmt_size, + H5S_sel_iter_t *iter); +__DLL__ hsize_t H5S_hyper_favail (const H5S_t *space, const H5S_sel_iter_t *iter, + hsize_t max); __DLL__ herr_t H5S_hyper_release(H5S_t *space); __DLL__ herr_t H5S_hyper_sel_iter_release(H5S_sel_iter_t *sel_iter); __DLL__ hsize_t H5S_hyper_npoints(const H5S_t *space); @@ -177,10 +175,9 @@ __DLL__ herr_t H5S_hyper_bounds(H5S_t *space, hsize_t *start, hsize_t *end); __DLL__ htri_t H5S_hyper_select_contiguous(const H5S_t *space); __DLL__ htri_t H5S_hyper_select_single(const H5S_t *space); __DLL__ htri_t H5S_hyper_select_regular(const H5S_t *space); -__DLL__ herr_t H5S_hyper_select_iterate(void *buf, hid_t type_id, H5S_t *space, - H5D_operator_t op, void *operator_data); -__DLL__ herr_t H5S_hyper_select_fill(const void *fill, size_t fill_size, - const H5S_t *space, void *buf); +__DLL__ herr_t H5S_hyper_select_get_seq_list(unsigned flags, const H5S_t *space,H5S_sel_iter_t *iter, + size_t elem_size, size_t maxseq, size_t maxbytes, + size_t *nseq, size_t *nbytes, hsize_t *off, size_t *len); /* "None" selection functions */ __DLL__ herr_t H5S_select_none(H5S_t *space); diff --git a/src/H5Spoint.c b/src/H5Spoint.c index 9dcfc4c..e7f32ef 100644 --- a/src/H5Spoint.c +++ b/src/H5Spoint.c @@ -10,61 +10,26 @@ #define H5S_PACKAGE /*suppress error about including H5Spkg */ -#include "H5private.h" -#include "H5Dprivate.h" -#include "H5Eprivate.h" -#include "H5Iprivate.h" -#include "H5MMprivate.h" -#include "H5Spkg.h" -#include "H5Tprivate.h" /* Datatypes */ -#include "H5Vprivate.h" +#include "H5private.h" /* Generic Functions */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5FLprivate.h" /* Free Lists */ +#include "H5Iprivate.h" /* ID Functions */ +#include "H5MMprivate.h" /* Memory Management functions */ +#include "H5Spkg.h" /* Dataspace functions */ +#include "H5Vprivate.h" /* Vector functions */ /* Interface initialization */ #define PABLO_MASK H5Spoint_mask #define INTERFACE_INIT NULL static int interface_initialize_g = 0; -static herr_t H5S_point_init (const H5S_t *space, size_t elmt_size, H5S_sel_iter_t *iter); -static hsize_t H5S_point_favail (const H5S_t *space, const H5S_sel_iter_t *iter, - hsize_t max); -static hsize_t H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, - size_t elmt_size, const H5S_t *file_space, - H5S_sel_iter_t *file_iter, hsize_t nelmts, - hid_t dxpl_id, void *buf/*out*/); -static herr_t H5S_point_fscat (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, - size_t elmt_size, const H5S_t *file_space, - H5S_sel_iter_t *file_iter, hsize_t nelmts, - hid_t dxpl_id, const void *buf); -static hsize_t H5S_point_mgath (const void *_buf, size_t elmt_size, - const H5S_t *mem_space, - H5S_sel_iter_t *mem_iter, hsize_t nelmts, - void *_tconv_buf/*out*/); -static herr_t H5S_point_mscat (const void *_tconv_buf, size_t elmt_size, - const H5S_t *mem_space, - H5S_sel_iter_t *mem_iter, hsize_t nelmts, - void *_buf/*out*/); - -const H5S_fconv_t H5S_POINT_FCONV[1] = {{ - "point", /*name */ - H5S_SEL_POINTS, /*selection type */ - H5S_point_init, /*initialize */ - H5S_point_favail, /*available */ - H5S_point_fgath, /*gather */ - H5S_point_fscat, /*scatter */ -}}; - -const H5S_mconv_t H5S_POINT_MCONV[1] = {{ - "point", /*name */ - H5S_SEL_POINTS, /*selection type */ - H5S_point_init, /*initialize */ - H5S_point_mgath, /*gather */ - H5S_point_mscat, /*scatter */ -}}; - - +/* Declare a free list to manage the H5S_pnt_node_t struct */ +H5FL_DEFINE_STATIC(H5S_pnt_node_t); +/* Declare a free list to manage the H5S_pnt_list_t struct */ +H5FL_DEFINE_STATIC(H5S_pnt_list_t); + + /*------------------------------------------------------------------------- * Function: H5S_point_init * @@ -79,7 +44,7 @@ const H5S_mconv_t H5S_POINT_MCONV[1] = {{ * *------------------------------------------------------------------------- */ -static herr_t +herr_t H5S_point_init (const H5S_t *space, size_t UNUSED elmt_size, H5S_sel_iter_t *sel_iter) { FUNC_ENTER_NOAPI(H5S_point_init, FAIL); @@ -134,7 +99,7 @@ herr_t H5S_point_add (H5S_t *space, H5S_seloper_t op, size_t num_elem, const hss top=curr=NULL; for(i=0; i<num_elem; i++) { /* Allocate space for the new node */ - if((new_node = H5MM_malloc(sizeof(H5S_pnt_node_t)))==NULL) + if((new_node = H5FL_ALLOC(H5S_pnt_node_t,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate point node"); @@ -199,7 +164,7 @@ done: * *------------------------------------------------------------------------- */ -static hsize_t +hsize_t H5S_point_favail (const H5S_t * UNUSED space, const H5S_sel_iter_t *sel_iter, hsize_t max) { @@ -211,337 +176,7 @@ H5S_point_favail (const H5S_t * UNUSED space, FUNC_LEAVE (MIN(sel_iter->pnt.elmt_left,max)); } /* H5S_point_favail() */ - -/*------------------------------------------------------------------------- - * Function: H5S_point_fgath - * - * Purpose: Gathers data points from file F and accumulates them in the - * type conversion buffer BUF. The LAYOUT argument describes - * how the data is stored on disk and EFL describes how the data - * is organized in external files. ELMT_SIZE is the size in - * bytes of a datum which this function treats as opaque. - * FILE_SPACE describes the data space of the dataset on disk - * and the elements that have been selected for reading (via - * hyperslab, etc). This function will copy at most NELMTS - * elements. - * - * Notes: This could be optimized by gathering selected elements near (how - * near?) each other into one I/O request and then moving the correct - * elements into the return buffer - * - * Return: Success: Number of elements copied. - * - * Failure: 0 - * - * Programmer: Quincey Koziol - * Tuesday, June 16, 1998 - * - * Modifications: - * Robb Matzke, 1999-08-03 - * The data transfer properties are passed by ID since that's - * what the virtual file layer needs. - *------------------------------------------------------------------------- - */ -static hsize_t -H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, - size_t elmt_size, const H5S_t *file_space, - H5S_sel_iter_t *file_iter, hsize_t nelmts, hid_t dxpl_id, - void *_buf/*out*/) -{ - hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ - hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ - hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ - uint8_t *buf=(uint8_t *)_buf; /* Alias for pointer arithmetic */ - unsigned ndims; /* Number of dimensions of dataset */ - unsigned u; /*counters */ - hsize_t num_read; /* number of elements read into buffer */ - FUNC_ENTER_NOAPI(H5S_point_fgath, 0); - - /* Check args */ - assert (f); - assert (layout); - assert (elmt_size>0); - assert (file_space); - assert (file_iter); - assert (nelmts>0); - assert (buf); - - ndims=file_space->extent.u.simple.rank; - /* initialize hyperslab size and offset in memory buffer */ - for(u=0; u<ndims+1; u++) { - hsize[u]=1; /* hyperslab size is 1, except for last element */ - zero[u]=0; /* memory offset is 0 */ - } /* end for */ - hsize[ndims] = elmt_size; - - /* - * Walk though and request each element we need and put it into the - * buffer. - */ - num_read=0; - while(num_read<nelmts) { - if(file_iter->pnt.elmt_left>0) { - /* Copy the location of the point to get */ - HDmemcpy(file_offset, file_iter->pnt.curr->pnt, ndims*sizeof(hssize_t)); - file_offset[ndims] = 0; - - /* Add in the offset */ - for(u=0; u<file_space->extent.u.simple.rank; u++) - file_offset[u] += file_space->select.offset[u]; - - /* Go read the point */ - if (H5F_arr_read(f, dxpl_id, layout, dc_plist, hsize, hsize, zero, file_offset, buf/*out*/)<0) - HRETURN_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); - - /* Increment the offset of the buffer */ - buf+=elmt_size; - - /* Increment the count read */ - num_read++; - - /* Advance the point iterator */ - file_iter->pnt.elmt_left--; - file_iter->pnt.curr=file_iter->pnt.curr->next; - } else { - break; /* out of elements in the selection */ - } /* end else */ - } /* end while */ - - FUNC_LEAVE (num_read); -} /* H5S_point_fgath() */ - -/*------------------------------------------------------------------------- - * Function: H5S_point_fscat - * - * Purpose: Scatters dataset elements from the type conversion buffer BUF - * to the file F where the data points are arranged according to - * the file data space FILE_SPACE and stored according to - * LAYOUT and EFL. Each element is ELMT_SIZE bytes. - * The caller is requesting that NELMTS elements are copied. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Tuesday, June 16, 1998 - * - * Modifications: - * Robb Matzke, 1999-08-03 - * The data transfer properties are passed by ID since that's - * what the virtual file layer needs. - *------------------------------------------------------------------------- - */ -static herr_t -H5S_point_fscat (H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, - size_t elmt_size, const H5S_t *file_space, - H5S_sel_iter_t *file_iter, hsize_t nelmts, hid_t dxpl_id, - const void *_buf) -{ - hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of hyperslab */ - hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ - hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero vector */ - const uint8_t *buf=(const uint8_t *)_buf; /* Alias for pointer arithmetic */ - unsigned ndims; /* Number of dimensions of dataset */ - unsigned u; /*counters */ - hsize_t num_written; /* number of elements written from buffer */ - - FUNC_ENTER_NOAPI(H5S_point_fscat, FAIL); - - /* Check args */ - assert (f); - assert (layout); - assert (elmt_size>0); - assert (file_space); - assert (file_iter); - assert (nelmts>0); - assert (buf); - - /* Hold the number of dimensions of the dataspace */ - ndims=file_space->extent.u.simple.rank; - - /* initialize hyperslab size and offset in memory buffer */ - for(u=0; u<ndims+1; u++) { - hsize[u]=1; /* hyperslab size is 1, except for last element */ - zero[u]=0; /* memory offset is 0 */ - } /* end for */ - hsize[ndims] = elmt_size; - - /* - * Walk though and request each element we need and put it into the - * buffer. - */ - num_written=0; - while(num_written<nelmts && file_iter->pnt.elmt_left>0) { - /* Copy the location of the point to get */ - HDmemcpy(file_offset,file_iter->pnt.curr->pnt,ndims*sizeof(hssize_t)); - file_offset[ndims] = 0; - - /* Add in the offset, if there is one */ - for(u=0; u<file_space->extent.u.simple.rank; u++) - file_offset[u] += file_space->select.offset[u]; - - /* Go write the point */ - if (H5F_arr_write(f, dxpl_id, layout, dc_plist, hsize, hsize, zero, file_offset, buf)<0) - HRETURN_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); - - /* Increment the offset of the buffer */ - buf+=elmt_size; - - /* Increment the count read */ - num_written++; - - /* Advance the point iterator */ - file_iter->pnt.elmt_left--; - file_iter->pnt.curr=file_iter->pnt.curr->next; - } /* end while */ - - FUNC_LEAVE (num_written>0 ? SUCCEED : FAIL); -} /* H5S_point_fscat() */ - -/*------------------------------------------------------------------------- - * Function: H5S_point_mgath - * - * Purpose: Gathers dataset elements from application memory BUF and - * copies them into the data type conversion buffer TCONV_BUF. - * Each element is ELMT_SIZE bytes and arranged in application - * memory according to MEM_SPACE. - * The caller is requesting that at most NELMTS be gathered. - * - * Return: Success: Number of elements copied. - * - * Failure: 0 - * - * Programmer: Quincey Koziol - * Tuesday, June 16, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hsize_t -H5S_point_mgath (const void *_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *_tconv_buf/*out*/) -{ - hsize_t mem_size[H5O_LAYOUT_NDIMS]; /*total size of app buf */ - const uint8_t *buf=(const uint8_t *)_buf; /* Get local copies for address arithmetic */ - uint8_t *tconv_buf=(uint8_t *)_tconv_buf; - hsize_t acc; /* coordinate accumulator */ - hsize_t off; /* coordinate offset */ - int space_ndims; /*dimensionality of space*/ - int i; /*counters */ - hsize_t num_gath; /* number of elements gathered */ - - FUNC_ENTER_NOAPI(H5S_point_mgath, 0); - - /* Check args */ - assert (buf); - assert (elmt_size>0); - assert (mem_space && H5S_SEL_POINTS==mem_space->select.type); - assert (nelmts>0); - assert (tconv_buf); - - /* Get the dataspace dimensions */ - if ((space_ndims=H5S_get_simple_extent_dims (mem_space, mem_size, NULL))<0) - HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, 0, "unable to retrieve data space dimensions"); - - /* Loop through all the points selected */ - for(num_gath=0; num_gath<nelmts; num_gath++) { - if(mem_iter->pnt.elmt_left>0) { - /* Compute the location of the point to get */ - for(i=space_ndims-1,acc=elmt_size,off=0; i>=0; i--) { - off+=(mem_iter->pnt.curr->pnt[i]+mem_space->select.offset[i])*acc; - acc*=mem_size[i]; - } /* end for */ - - /* Copy the elements into the type conversion buffer */ - HDmemcpy(tconv_buf,buf+off,elmt_size); - - /* Increment the offset of the buffers */ - tconv_buf+=elmt_size; - - /* Advance the point iterator */ - mem_iter->pnt.elmt_left--; - mem_iter->pnt.curr=mem_iter->pnt.curr->next; - } else { - break; /* out of elements in the selection */ - } /* end else */ - } /* end for */ - - FUNC_LEAVE (num_gath); -} /* H5S_point_mgath() */ - -/*------------------------------------------------------------------------- - * Function: H5S_point_mscat - * - * Purpose: Scatters NELMTS data points from the type conversion buffer - * TCONV_BUF to the application buffer BUF. Each element is - * ELMT_SIZE bytes and they are organized in application memory - * according to MEM_SPACE. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Wednesday, June 17, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static herr_t -H5S_point_mscat (const void *_tconv_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *_buf/*out*/) -{ - hsize_t mem_size[H5O_LAYOUT_NDIMS]; /*total size of app buf */ - uint8_t *buf=(uint8_t *)_buf; /* Get local copies for address arithmetic */ - const uint8_t *tconv_buf=(const uint8_t *)_tconv_buf; - hsize_t acc; /* coordinate accumulator */ - hsize_t off; /* coordinate offset */ - int space_ndims; /*dimensionality of space*/ - int i; /*counters */ - hsize_t num_scat; /* Number of elements scattered */ - - FUNC_ENTER_NOAPI(H5S_point_mscat, FAIL); - - /* Check args */ - assert (tconv_buf); - assert (elmt_size>0); - assert (mem_space && H5S_SEL_POINTS==mem_space->select.type); - assert (nelmts>0); - assert (buf); - - /* Get the dataspace dimensions */ - if ((space_ndims=H5S_get_simple_extent_dims (mem_space, mem_size, NULL))<0) - HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to retrieve data space dimensions"); - - /* Loop through all the points selected */ - for(num_scat=0; num_scat<nelmts; num_scat++) { - if(mem_iter->pnt.elmt_left>0) { - /* Compute the location of the point to get */ - for(i=space_ndims-1,acc=elmt_size,off=0; i>=0; i--) { - off+=(mem_iter->pnt.curr->pnt[i]+mem_space->select.offset[i])*acc; - acc*=mem_size[i]; - } /* end for */ - - /* Copy the elements into the type conversion buffer */ - HDmemcpy(buf+off,tconv_buf,elmt_size); - - /* Increment the offset of the buffers */ - tconv_buf+=elmt_size; - - /* Advance the point iterator */ - mem_iter->pnt.elmt_left--; - mem_iter->pnt.curr=mem_iter->pnt.curr->next; - } else { - break; /* out of elements in the selection */ - } /* end else */ - } /* end for */ - - FUNC_LEAVE (SUCCEED); -} /* H5S_point_mscat() */ /*-------------------------------------------------------------------------- NAME @@ -575,12 +210,12 @@ H5S_point_release (H5S_t *space) while(curr!=NULL) { next=curr->next; H5MM_xfree(curr->pnt); - H5MM_xfree(curr); + H5FL_FREE(H5S_pnt_node_t,curr); curr=next; } /* end while */ /* Free & reset the point list header */ - H5MM_xfree(space->select.sel_info.pnt_lst); + H5FL_FREE(H5S_pnt_list_t,space->select.sel_info.pnt_lst); space->select.sel_info.pnt_lst=NULL; /* Reset the number of elements in the selection */ @@ -588,6 +223,7 @@ H5S_point_release (H5S_t *space) FUNC_LEAVE (SUCCEED); } /* H5S_point_release() */ + /*-------------------------------------------------------------------------- NAME @@ -616,6 +252,7 @@ H5S_point_npoints (const H5S_t *space) FUNC_LEAVE (space->select.num_elem); } /* H5S_point_npoints() */ + /*-------------------------------------------------------------------------- NAME @@ -648,7 +285,7 @@ H5S_point_copy (H5S_t *dst, const H5S_t *src) assert(dst); /* Allocate room for the head of the point list */ - if((dst->select.sel_info.pnt_lst=H5MM_malloc(sizeof(H5S_pnt_list_t)))==NULL) + if((dst->select.sel_info.pnt_lst=H5FL_ALLOC(H5S_pnt_list_t,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate point node"); @@ -656,7 +293,7 @@ H5S_point_copy (H5S_t *dst, const H5S_t *src) new_head=NULL; while(curr!=NULL) { /* Create each point */ - if((new_node=H5MM_malloc(sizeof(H5S_pnt_node_t)))==NULL) + if((new_node=H5FL_ALLOC(H5S_pnt_node_t,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate point node"); if((new_node->pnt = H5MM_malloc(src->extent.u.simple.rank*sizeof(hssize_t)))==NULL) @@ -679,6 +316,7 @@ H5S_point_copy (H5S_t *dst, const H5S_t *src) done: FUNC_LEAVE (ret_value); } /* end H5S_point_copy() */ + /*-------------------------------------------------------------------------- NAME @@ -730,6 +368,7 @@ H5S_point_select_valid (const H5S_t *space) FUNC_LEAVE (ret_value); } /* end H5S_point_select_valid() */ + /*-------------------------------------------------------------------------- NAME @@ -776,6 +415,7 @@ H5S_point_select_serial_size (const H5S_t *space) FUNC_LEAVE (ret_value); } /* end H5S_point_select_serial_size() */ + /*-------------------------------------------------------------------------- NAME @@ -845,6 +485,7 @@ H5S_point_select_serialize (const H5S_t *space, uint8_t *buf) FUNC_LEAVE (ret_value); } /* H5S_point_select_serialize() */ + /*-------------------------------------------------------------------------- NAME @@ -909,6 +550,7 @@ done: FUNC_LEAVE (ret_value); } /* H5S_point_select_deserialize() */ + /*-------------------------------------------------------------------------- NAME @@ -1134,13 +776,13 @@ herr_t H5S_select_elements (H5S_t *space, H5S_seloper_t op, size_t num_elem, if(op==H5S_SELECT_SET) { if(H5S_select_release(space)<0) { HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, - "can't release hyperslab"); + "can't release point selection"); } /* end if */ } /* end if */ /* Allocate space for the point selection information if necessary */ if(space->select.type!=H5S_SEL_POINTS || space->select.sel_info.pnt_lst==NULL) { - if((space->select.sel_info.pnt_lst = H5MM_calloc(sizeof(H5S_pnt_list_t)))==NULL) + if((space->select.sel_info.pnt_lst = H5FL_ALLOC(H5S_pnt_list_t,1))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate element information"); } /* end if */ @@ -1222,161 +864,141 @@ done: /*-------------------------------------------------------------------------- NAME - H5S_point_select_iterate + H5S_point_select_get_seq_list PURPOSE - Iterate over a point selection, calling a user's function for each - element. + Create a list of offsets & lengths for a selection USAGE - herr_t H5S_point_select_iterate(buf, type_id, space, op, operator_data) - void *buf; IN/OUT: Buffer containing elements to iterate over - hid_t type_id; IN: Datatype ID of BUF array. - H5S_t *space; IN: Dataspace object containing selection to iterate over - H5D_operator_t op; IN: Function pointer to the routine to be - called for each element in BUF iterated over. - void *operator_data; IN/OUT: Pointer to any user-defined data - associated with the operation. - RETURNS - Returns the return value of the last operator if it was non-zero, or zero - if all elements were processed. Otherwise returns a negative value. - DESCRIPTION - Iterates over the selected elements in a memory buffer, calling the user's - callback function for each element. The selection in the dataspace is - modified so that any elements already iterated over are removed from the - selection if the iteration is interrupted (by the H5D_operator_t function - returning non-zero) in the "middle" of the iteration and may be re-started - by the user where it left off. - - NOTE: Until "subtracting" elements from a selection is implemented, - the selection is not modified. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG - QAK - 2002/4/5 - Wasn't using selection offset in calculation, corrected. ---------------------------------------------------------------------------*/ -herr_t -H5S_point_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op, - void *operator_data) -{ - hsize_t mem_size[H5O_LAYOUT_NDIMS]; /* Dataspace size */ - hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /* Point offset */ - hsize_t offset; /* Offset of region in buffer */ - void *tmp_buf; /* Temporary location of the element in the buffer */ - H5S_pnt_node_t *node; /* Point node */ - unsigned rank; /* Dataspace rank */ - H5T_t *dt; /* Datatype structure */ - unsigned u; /* Local index variable */ - herr_t ret_value=0; /* return value */ - - FUNC_ENTER_NOAPI(H5S_point_select_iterate, 0); - - assert(buf); - assert(space); - assert(op); - assert(H5I_DATATYPE == H5I_get_type(type_id)); - - /* Get the dataspace extent rank */ - rank=space->extent.u.simple.rank; - - /* Set up the size of the memory space */ - HDmemcpy(mem_size, space->extent.u.simple.size, rank*sizeof(hsize_t)); - - /* Set the size of the datatype */ - if (NULL==(dt=H5I_object(type_id))) - HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype"); - mem_size[rank]=H5T_get_size(dt); - - /* Iterate through the node, checking the bounds on each element */ - node=space->select.sel_info.pnt_lst->head; - while(node!=NULL && ret_value==0) { - /* Set up the location of the point */ - HDmemcpy(mem_offset, node->pnt, rank*sizeof(hssize_t)); - mem_offset[rank]=0; - - /* Add in the selection offset */ - for(u=0; u<rank; u++) - mem_offset[u]+=space->select.offset[u]; - - /* Get the offset in the memory buffer */ - offset=H5V_array_offset(rank+1,mem_size,(const hssize_t *)mem_offset); - tmp_buf=((char *)buf+offset); - - ret_value=(*op)(tmp_buf,type_id,(hsize_t)rank,mem_offset,operator_data); - - node=node->next; - } /* end while */ - - FUNC_LEAVE (ret_value); -} /* H5S_point_select_iterate() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S_point_select_fill - PURPOSE - Fill a point selection in memory with a value - USAGE - herr_t H5S_point_select_fill(fill,fill_size,space,buf) - const void *fill; IN: Pointer to fill value to use - size_t fill_size; IN: Size of elements in memory buffer & size of - fill value - H5S_t *space; IN: Dataspace describing memory buffer & - containing selection to use. - void *buf; IN/OUT: Memory buffer to fill selection in + herr_t H5S_point_select_get_seq_list(flags,space,iter,elem_size,maxseq,maxbytes,nseq,nbytes,off,len) + unsigned flags; IN: Flags for extra information about operation + H5S_t *space; IN: Dataspace containing selection to use. + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + size_t elem_size; IN: Size of an element + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxbytes; IN: Maximum number of bytes to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + size_t *nbytes; OUT: Actual number of bytes in sequences generated + hsize_t *off; OUT: Array of offsets + size_t *len; OUT: Array of lengths RETURNS Non-negative on success/Negative on failure. DESCRIPTION - Use the selection in the dataspace to fill elements in a memory buffer. + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS - The memory buffer elements are assumed to have the same datatype as the - fill value being placed into them. EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ herr_t -H5S_point_select_fill(const void *fill, size_t fill_size, const H5S_t *space, void *_buf) +H5S_point_select_get_seq_list(unsigned flags, const H5S_t *space,H5S_sel_iter_t *iter, + size_t elem_size, size_t maxseq, size_t maxbytes, size_t *nseq, size_t *nbytes, + hsize_t *off, size_t *len) { - hsize_t size[H5O_LAYOUT_NDIMS]; /* Total size of memory buf */ - uint8_t *buf=(uint8_t *)_buf; /* Alias for memory buffer */ - hsize_t acc; /* Coordinate accumulator */ - hsize_t off; /* Coordinate offset */ + hsize_t bytes_left; /* The number of bytes left in the selection */ + hsize_t start_bytes_left; /* The initial number of bytes left in the selection */ H5S_pnt_node_t *node; /* Point node */ + hsize_t dims[H5O_LAYOUT_NDIMS]; /* Total size of memory buf */ int ndims; /* Dimensionality of space*/ - int i; /* Index variable */ - herr_t ret_value=SUCCEED; /* return value */ + hsize_t acc; /* Coordinate accumulator */ + hsize_t loc; /* Coordinate offset */ + size_t curr_seq; /* Current sequence being operated on */ + int i; /* Local index variable */ + herr_t ret_value=SUCCEED; /* return value */ - FUNC_ENTER_NOAPI(H5S_point_select_fill, FAIL); + FUNC_ENTER_NOAPI (H5S_point_select_get_seq_list, FAIL); /* Check args */ - assert(fill); - assert(fill_size>0); assert(space); - assert(buf); + assert(iter); + assert(elem_size>0); + assert(maxseq>0); + assert(maxbytes>0); + assert(nseq); + assert(nbytes); + assert(off); + assert(len); - /* Fill the selection in the memory buffer */ + /* "round" off the maxbytes allowed to a multiple of the element size */ + maxbytes=(maxbytes/elem_size)*elem_size; + + /* Choose the minimum number of bytes to sequence through */ + start_bytes_left=bytes_left=MIN(iter->pnt.elmt_left*elem_size,maxbytes); /* Get the dataspace dimensions */ - if ((ndims=H5S_get_simple_extent_dims (space, size, NULL))<0) + if ((ndims=H5S_get_simple_extent_dims (space, dims, NULL))<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to retrieve data space dimensions"); - /* Loop through all the points selected */ - node=space->select.sel_info.pnt_lst->head; + /* Walk through the points in the selection, starting at the current */ + /* location in the iterator */ + node=iter->pnt.curr; + curr_seq=0; while(node!=NULL) { /* Compute the offset of each selected point in the buffer */ - for(i=ndims-1,acc=fill_size,off=0; i>=0; i--) { - off+=(node->pnt[i]+space->select.offset[i])*acc; - acc*=size[i]; + for(i=ndims-1,acc=elem_size,loc=0; i>=0; i--) { + loc+=(node->pnt[i]+space->select.offset[i])*acc; + acc*=dims[i]; } /* end for */ - /* Set the selected point to the fill value */ - HDmemcpy(buf+off,fill,fill_size); + /* Check if this is a later point in the selection */ + if(curr_seq>0) { + /* If a sorted sequence is requested, make certain we don't go backwards in the offset */ + if((flags&H5S_GET_SEQ_LIST_SORTED) && loc<off[curr_seq-1]) + break; + + /* Check if this point extends the previous sequence */ + /* (Unlikely, but possible) */ + if(loc==(off[curr_seq-1]+len[curr_seq-1])) { + /* Extend the previous sequence */ + len[curr_seq-1]+=elem_size; + } /* end if */ + else { + /* Add a new sequence */ + off[curr_seq]=loc; + len[curr_seq]=elem_size; + + /* Increment sequence count */ + curr_seq++; + } /* end else */ + } /* end if */ + else { + /* Add a new sequence */ + off[curr_seq]=loc; + len[curr_seq]=elem_size; + + /* Increment sequence count */ + curr_seq++; + } /* end else */ + + /* Decrement number of bytes left to process */ + bytes_left-=elem_size; + + /* Move the iterator */ + iter->pnt.curr=node->next; + iter->pnt.elmt_left--; + + /* Check if we're finished with all sequences */ + if(curr_seq==maxseq) + break; + + /* Check if we're finished with all the bytes available */ + if(bytes_left==0) + break; /* Advance to the next point */ node=node->next; } /* end while */ + /* Set the number of sequences generated */ + *nseq=curr_seq; + + /* Set the number of bytes used */ + *nbytes=(start_bytes_left-bytes_left); + done: FUNC_LEAVE (ret_value); -} /* H5S_point_select_fill() */ - +} /* end H5S_point_select_get_seq_list() */ diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index de7f838..1412ea3 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -40,11 +40,15 @@ #define H5S_CONV_STORAGE_CHUNKED 0x0004 /* i.e. '2' */ #define H5S_CONV_STORAGE_MASK 0x0006 +/* Flags for H5S_select_get_seq_list() */ +#define H5S_GET_SEQ_LIST_SORTED 0x0001 + /* Forward references of common typedefs */ typedef struct H5S_t H5S_t; typedef struct H5S_pnt_node_t H5S_pnt_node_t; typedef struct H5S_hyper_span_t H5S_hyper_span_t; typedef struct H5S_hyper_span_info_t H5S_hyper_span_info_t; +typedef struct H5S_hyper_dim_t H5S_hyper_dim_t; /* Point selection iteration container */ typedef struct { @@ -54,10 +58,24 @@ typedef struct { /* New Hyperslab selection iteration container */ typedef struct { + /* Common fields for all hyperslab selections */ hsize_t elmt_left; /* Number of elements left to iterate over */ + hssize_t *off; /* Offset in span node (used as position for regular hyperslabs) */ + unsigned iter_rank; /* Rank of iterator information */ + /* (This should always be the same as the dataspace + * rank, except for regular hyperslab selections in + * which there are contiguous regions in the lower + * dimensions which have been "flattened" out + */ + + /* "Flattened" regular hyperslab selection fields */ + H5S_hyper_dim_t *diminfo; /* "Flattened" regular selection information */ + hsize_t *size; /* "Flattened" dataspace extent information */ + hssize_t *sel_off; /* "Flattened" selection offset information */ + + /* Irregular hyperslab selection fields */ H5S_hyper_span_info_t *spans; /* Pointer to copy of the span tree */ - H5S_hyper_span_t **span; /* Array of pointers to span nodes */ - hssize_t *off; /* Offset in span node (position for regular hyperslabs) */ + H5S_hyper_span_t **span;/* Array of pointers to span nodes */ } H5S_hyper_iter_t; /* "All" selection iteration container */ @@ -73,59 +91,9 @@ typedef union { H5S_all_iter_t all; /* "All" selection iteration information */ } H5S_sel_iter_t; -/* - * Data space conversions usually take place in two halves. One half - * transfers data points between memory and a data type conversion array - * where the points are contiguous, and the other half transfers points - * between the type conversion array and the file. - */ -typedef struct H5S_fconv_t { - /* Identification */ - const char *name; - H5S_sel_type type; - - /* Initialize file element numbering information */ - herr_t (*init)(const H5S_t *space, size_t elmt_size, H5S_sel_iter_t *iter); - - /* Determine optimal number of elements to transfer */ - hsize_t (*avail)(const H5S_t *file_space, const H5S_sel_iter_t *file_iter, - hsize_t max); - - /* Gather elements from disk to type conversion buffer */ - hsize_t (*gath)(H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, H5S_sel_iter_t *file_iter, - hsize_t nelmts, hid_t dxpl_id, void *tconv_buf/*out*/); - - /* Scatter elements from type conversion buffer to disk */ - herr_t (*scat)(H5F_t *f, const struct H5O_layout_t *layout, - H5P_genplist_t *dc_plist, size_t elmt_size, - const H5S_t *file_space, H5S_sel_iter_t *file_iter, - hsize_t nelmts, hid_t dxpl_id, const void *tconv_buf); -} H5S_fconv_t; - -typedef struct H5S_mconv_t { - /* Identification */ - const char *name; - H5S_sel_type type; - - /* Initialize memory element numbering information */ - herr_t (*init)(const H5S_t *space, size_t elmt_size, H5S_sel_iter_t *iter); - - /* Gather elements from app buffer to type conversion buffer */ - hsize_t (*gath)(const void *buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *tconv_buf/*out*/); - - /* Scatter elements from type conversion buffer to application buffer */ - herr_t (*scat)(const void *tconv_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *buf/*out*/); -} H5S_mconv_t; - typedef struct H5S_conv_t { - const H5S_fconv_t *f; - const H5S_mconv_t *m; + H5S_sel_type ftype; + H5S_sel_type mtype; /* * If there is no data type conversion then it might be possible to @@ -167,14 +135,6 @@ typedef struct H5S_conv_t { #endif } H5S_conv_t; -/* Conversion information for the various data space selection types */ -__DLLVAR__ const H5S_fconv_t H5S_POINT_FCONV[]; -__DLLVAR__ const H5S_mconv_t H5S_POINT_MCONV[]; -__DLLVAR__ const H5S_fconv_t H5S_ALL_FCONV[]; -__DLLVAR__ const H5S_mconv_t H5S_ALL_MCONV[]; -__DLLVAR__ const H5S_fconv_t H5S_HYPER_FCONV[]; -__DLLVAR__ const H5S_mconv_t H5S_HYPER_MCONV[]; - /* We get the declaration of H5G_entry_t from the H5Oprivate.h file */ __DLL__ H5S_t *H5S_create(H5S_class_t type); @@ -215,10 +175,37 @@ __DLL__ htri_t H5S_select_regular(const H5S_t *space); __DLL__ htri_t H5S_select_shape_same(const H5S_t *space1, const H5S_t *space2); __DLL__ herr_t H5S_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op, void *operator_data); +__DLL__ herr_t H5S_select_iter_init(const H5S_t *space, size_t elmt_size, + H5S_sel_iter_t *iter); __DLL__ herr_t H5S_sel_iter_release(const H5S_t *space, H5S_sel_iter_t *sel_iter); __DLL__ herr_t H5S_select_fill(void *fill, size_t fill_size, const H5S_t *space, void *buf); +__DLL__ herr_t H5S_select_get_seq_list(unsigned flags, const H5S_t *space,H5S_sel_iter_t *iter, + size_t elem_size, size_t maxseq, size_t maxbytes, + size_t *nseq, size_t *nbytes, hsize_t *off, size_t *len); +__DLL__ hsize_t H5S_select_favail(const H5S_t *space, const H5S_sel_iter_t *iter, + hsize_t max); +__DLL__ herr_t H5S_select_fscat (H5F_t *f, const struct H5O_layout_t *layout, + H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space, + H5S_sel_iter_t *file_iter, hsize_t nelmts, hid_t dxpl_id, + const void *_buf); +__DLL__ hsize_t H5S_select_fgath (H5F_t *f, const struct H5O_layout_t *layout, + H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space, + H5S_sel_iter_t *file_iter, hsize_t nelmts, hid_t dxpl_id, + void *buf); +__DLL__ herr_t H5S_select_mscat (const void *_tscat_buf, size_t elmt_size, + const H5S_t *space, H5S_sel_iter_t *iter, hsize_t nelmts, + hid_t dxpl_id, void *_buf/*out*/); +__DLL__ hsize_t H5S_select_mgath (const void *_buf, size_t elmt_size, + const H5S_t *space, H5S_sel_iter_t *iter, hsize_t nelmts, + hid_t dxpl_id, void *_tgath_buf/*out*/); +__DLL__ herr_t H5S_select_read(H5F_t *f, const struct H5O_layout_t *layout, + H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space, + const H5S_t *mem_space, hid_t dxpl_id, void *buf/*out*/); +__DLL__ herr_t H5S_select_write(H5F_t *f, const struct H5O_layout_t *layout, + H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space, + const H5S_t *mem_space, hid_t dxpl_id, const void *buf/*out*/); /* Needed for internal use of selections in H5Fistore code */ __DLL__ herr_t H5S_select_all(H5S_t *space); diff --git a/src/H5Sselect.c b/src/H5Sselect.c index c4a6bdb..7c239bb 100644 --- a/src/H5Sselect.c +++ b/src/H5Sselect.c @@ -10,13 +10,13 @@ #define H5S_PACKAGE /*suppress error about including H5Spkg */ -#include "H5private.h" -#include "H5Eprivate.h" -#include "H5FLprivate.h" /*Free Lists */ -#include "H5Iprivate.h" -#include "H5MMprivate.h" -#include "H5Spkg.h" -#include "H5Vprivate.h" +#include "H5private.h" /* Generic Functions */ +#include "H5Dprivate.h" /* Datasets (for their properties) */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5FLprivate.h" /* Free Lists */ +#include "H5Iprivate.h" /* ID Functions */ +#include "H5Spkg.h" /* Dataspace functions */ +#include "H5Vprivate.h" /* Vector functions */ /* Interface initialization */ #define PABLO_MASK H5Sselect_mask @@ -32,6 +32,18 @@ static herr_t H5S_get_select_bounds(H5S_t *space, hsize_t *start, hsize_t *end); /* Declare external the free list for hssize_t arrays */ H5FL_ARR_EXTERN(hssize_t); +/* Declare a free list to manage arrays of size_t */ +H5FL_ARR_DEFINE_STATIC(size_t,-1); + +/* Declare a free list to manage arrays of hsize_t */ +H5FL_ARR_DEFINE_STATIC(hsize_t,-1); + +/* Declare a free list to manage the H5S_sel_iter_t struct */ +H5FL_DEFINE_STATIC(H5S_sel_iter_t); + +/* Declare a free list to manage blocks of single datatype element data */ +H5FL_BLK_EXTERN(type_elem); + /*-------------------------------------------------------------------------- NAME @@ -207,6 +219,7 @@ H5Sget_select_npoints(hid_t spaceid) FUNC_LEAVE (ret_value); } /* H5Sget_select_npoints() */ + /*-------------------------------------------------------------------------- NAME @@ -258,6 +271,7 @@ H5S_get_select_npoints (const H5S_t *space) FUNC_LEAVE (ret_value); } /* H5S_get_select_npoints() */ + /*-------------------------------------------------------------------------- NAME @@ -1220,6 +1234,59 @@ H5S_select_contiguous(const H5S_t *space) /*-------------------------------------------------------------------------- NAME + H5S_select_iter_init + PURPOSE + Construct an iterator for a dataspace & selection + USAGE + herr_t H5S_select_iter_init(space, elmt_size, iter) + H5S_t *space; IN: Dataspace object containing selection to iterate over + size_t elmt_size; IN: Size of element in dataspace + H5S_sel_iter_t *iter; OUT: Iterator to initialize + RETURNS + Non-negative on success, negative on failure + DESCRIPTION + Genericly initializes an iterator, based on the type of selection in the + dataspace. +--------------------------------------------------------------------------*/ +herr_t +H5S_select_iter_init(const H5S_t *space, size_t elmt_size, H5S_sel_iter_t *iter) +{ + herr_t ret_value=FAIL; /* return value */ + + FUNC_ENTER_NOINIT(H5S_select_iter_init); + + assert(space); + assert(iter); + + /* Initialize iterator */ + switch(space->select.type) { + case H5S_SEL_POINTS: /* Sequence of points selected */ + ret_value=H5S_point_init(space,elmt_size,iter); + break; + + case H5S_SEL_HYPERSLABS: /* Hyperslab selection defined */ + ret_value=H5S_hyper_init(space,elmt_size,iter); + break; + + case H5S_SEL_ALL: /* Entire extent selected */ + ret_value=H5S_all_init(space,elmt_size,iter); + break; + + case H5S_SEL_NONE: /* Nothing selected */ + ret_value=FALSE; + break; + + case H5S_SEL_ERROR: + case H5S_SEL_N: + break; + } + + FUNC_LEAVE (ret_value); +} /* end H5S_select_iter_init() */ + + +/*-------------------------------------------------------------------------- + NAME H5S_select_iterate PURPOSE Iterate over the selected elements in a memory buffer. @@ -1250,37 +1317,137 @@ herr_t H5S_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op, void *operator_data) { - herr_t ret_value=FAIL; + H5T_t *dt; /* Datatype structure */ + H5P_genplist_t *dx_plist; /* Dataset transfer property list */ + H5S_sel_iter_t *iter=NULL; /* Selection iteration info */ + uint8_t *loc; /* Current element location in buffer */ + hssize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of element in dataspace */ + hssize_t nelmts; /* Number of elements in selection */ + hsize_t space_size[H5O_LAYOUT_NDIMS]; /* Dataspace size */ + hsize_t *off=NULL; /* Array to store sequence offsets */ + hsize_t curr_off; /* Current offset within sequence */ + hsize_t tmp_off; /* Temporary offset within sequence */ + size_t *len=NULL; /* Array to store sequence lengths */ + size_t curr_len; /* Length of bytes left to process in sequence */ + size_t vector_size; /* Value for vector size */ + size_t nseq; /* Number of sequences generated */ + size_t curr_seq; /* Current sequnce being worked on */ + size_t nbytes; /* Number of bytes used in sequences */ + size_t max_bytes; /* Maximum number of bytes allowed in sequences */ + size_t elmt_size; /* Datatype size */ + int ndims; /* Number of dimensions in dataspace */ + int i; /* Local Index variable */ + herr_t user_ret=0; /* User's return value */ + herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5S_select_iterate, FAIL); /* Check args */ assert(buf); + assert(H5I_DATATYPE == H5I_get_type(type_id)); assert(space); assert(op); - assert(H5I_DATATYPE == H5I_get_type(type_id)); - switch(space->select.type) { - case H5S_SEL_POINTS: /* Sequence of points selected */ - ret_value=H5S_point_select_iterate(buf,type_id,space,op,operator_data); - break; + /* Get the hyperslab vector size */ + /* (from the default data transfer property list, for now) */ + dx_plist = H5I_object(H5P_DATASET_XFER_DEFAULT); + assert(dx_plist); + if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value"); + + /* Allocate the vector I/O arrays */ + if((len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); + if((off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); + + /* Get the datatype size */ + if (NULL==(dt=H5I_object(type_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype"); + if((elmt_size=H5T_get_size(dt))==0) + HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid"); + + /* Allocate iterator */ + if((iter = H5FL_ALLOC(H5S_sel_iter_t,1))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate selection iterator"); + + /* Initialize iterator */ + if (H5S_select_iter_init(space, elmt_size, iter)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); + + /* Get the number of elements in selection */ + if((nelmts = H5S_get_select_npoints(space))<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements selected"); + + /* Get the rank of the dataspace */ + ndims=space->extent.u.simple.rank; + + /* Copy the size of the space */ + assert(space->extent.u.simple.size); + assert(ndims>0); + HDmemcpy(space_size, space->extent.u.simple.size, ndims*sizeof(hsize_t)); + space_size[ndims]=elmt_size; + + /* Compute the maximum number of bytes required */ + H5_ASSIGN_OVERFLOW(max_bytes,nelmts*elmt_size,hsize_t,size_t); + + /* Loop, while elements left in selection */ + while(max_bytes>0 && user_ret==0) { + /* Get the sequences of bytes */ + if(H5S_select_get_seq_list(0,space,iter,elmt_size,vector_size,max_bytes,&nseq,&nbytes,off,len)<0) + HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); + + /* Loop, while sequences left to process */ + for(curr_seq=0; curr_seq<nseq && user_ret==0; curr_seq++) { + /* Get the current offset */ + curr_off=off[curr_seq]; + + /* Get the number of bytes in sequence */ + curr_len=len[curr_seq]; + + /* Loop, while bytes left in sequence */ + while(curr_len>0 && user_ret==0) { + /* Compute the coordinate from the offset */ + for(i=ndims, tmp_off=curr_off; i>=0; i--) { + coords[i]=tmp_off%space_size[i]; + tmp_off/=space_size[i]; + } /* end for */ + + /* Get the location within the user's buffer */ + loc=(unsigned char *)buf+curr_off; + + /* Call user's callback routine */ + user_ret=(*op)(loc,type_id,(hsize_t)ndims,coords,operator_data); + + /* Increment offset in dataspace */ + curr_off+=elmt_size; + + /* Decrement number of bytes left in sequence */ + curr_len-=elmt_size; + } /* end while */ + } /* end for */ - case H5S_SEL_HYPERSLABS: /* Hyperslab selection defined */ - ret_value=H5S_hyper_select_iterate(buf,type_id,space,op,operator_data); - break; + /* Decrement number of elements left to process */ + assert((nbytes%elmt_size)==0); + max_bytes-=nbytes; + } /* end while */ - case H5S_SEL_ALL: /* Entire extent selected */ - ret_value=H5S_all_select_iterate(buf,type_id,space,op,operator_data); - break; + /* Set return value */ + ret_value=user_ret; - case H5S_SEL_NONE: /* Nothing selected */ - ret_value=H5S_none_select_iterate(buf,type_id,space,op,operator_data); - break; +done: + /* Release selection iterator */ + if(iter!=NULL) { + if (H5S_sel_iter_release(space, iter)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); + H5FL_FREE(H5S_sel_iter_t,iter); + } /* end if */ - case H5S_SEL_ERROR: - case H5S_SEL_N: - break; - } + /* Release length & offset vectors */ + if(len!=NULL) + H5FL_ARR_FREE(size_t,len); + if(off!=NULL) + H5FL_ARR_FREE(hsize_t,off); FUNC_LEAVE(ret_value); } /* end H5S_select_iterate() */ @@ -1565,10 +1732,21 @@ H5S_select_regular(const H5S_t *space) REVISION LOG --------------------------------------------------------------------------*/ herr_t -H5S_select_fill(void *_fill, size_t fill_size, const H5S_t *space, void *buf) +H5S_select_fill(void *_fill, size_t fill_size, const H5S_t *space, void *_buf) { + H5P_genplist_t *dx_plist; /* Dataset transfer property list */ + H5S_sel_iter_t *iter=NULL; /* Selection iteration info */ + uint8_t *buf; /* Current location in buffer */ void *fill=_fill; /* Alias for fill-value buffer */ - herr_t ret_value=FAIL; /* return value */ + hssize_t nelmts; /* Number of elements in selection */ + hsize_t *off=NULL; /* Array to store sequence offsets */ + size_t *len=NULL; /* Array to store sequence lengths */ + size_t vector_size; /* Value for vector size */ + size_t nseq; /* Number of sequences generated */ + size_t curr_seq; /* Current sequnce being worked on */ + size_t nbytes; /* Number of bytes used in sequences */ + size_t max_bytes; /* Total number of bytes in selection */ + herr_t ret_value=SUCCEED; /* return value */ FUNC_ENTER_NOAPI(H5S_select_fill, FAIL); @@ -1579,27 +1757,151 @@ H5S_select_fill(void *_fill, size_t fill_size, const H5S_t *space, void *buf) /* Check if we need a temporary fill value buffer */ if(fill==NULL) { - if (NULL==(fill = H5MM_calloc(fill_size))) + if (NULL==(fill = H5FL_BLK_ALLOC(type_elem,fill_size,1))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "fill value buffer allocation failed"); } /* end if */ - /* Fill the selection in the memory buffer */ + /* Get the hyperslab vector size */ + /* (from the default data transfer property list, for now) */ + dx_plist = H5I_object(H5P_DATASET_XFER_DEFAULT); + assert(dx_plist); + if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value"); + + /* Allocate the vector I/O arrays */ + if((len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); + if((off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); + + /* Allocate iterator */ + if((iter = H5FL_ALLOC(H5S_sel_iter_t,1))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate selection iterator"); + + /* Initialize iterator */ + if (H5S_select_iter_init(space, fill_size, iter)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); + + /* Get the number of elements in selection */ + if((nelmts = H5S_get_select_npoints(space))<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements selected"); + + /* Compute the number of bytes to process */ + H5_CHECK_OVERFLOW(nelmts,hssize_t,size_t); + max_bytes=(size_t)nelmts*fill_size; + + /* Loop, while elements left in selection */ + while(max_bytes>0) { + /* Get the sequences of bytes */ + if(H5S_select_get_seq_list(0,space,iter,fill_size,vector_size,max_bytes,&nseq,&nbytes,off,len)<0) + HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); + + /* Loop over sequences */ + for(curr_seq=0; curr_seq<nseq; curr_seq++) { + /* Get offset in memory buffer */ + buf=(uint8_t *)_buf+off[curr_seq]; + + /* Fill each sequence in memory with fill value */ + assert((len[curr_seq]%fill_size)==0); + H5V_array_fill(buf, fill, fill_size, (len[curr_seq]/fill_size)); + } /* end for */ + + /* Decrement number of bytes left to process */ + max_bytes-=nbytes; + } /* end while */ + +done: + /* Release selection iterator */ + if(iter!=NULL) { + if (H5S_sel_iter_release(space, iter)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); + H5FL_FREE(H5S_sel_iter_t,iter); + } /* end if */ + + /* Release length & offset vectors */ + if(len!=NULL) + H5FL_ARR_FREE(size_t,len); + if(off!=NULL) + H5FL_ARR_FREE(hsize_t,off); + + /* Release fill value, if allocated */ + if(_fill==NULL && fill) + H5FL_BLK_FREE(type_elem,fill); + + FUNC_LEAVE (ret_value); +} /* H5S_select_fill() */ + + +/*-------------------------------------------------------------------------- + NAME + H5S_select_get_seq_list + PURPOSE + Create a list of offsets & lengths for a selection + USAGE + herr_t H5S_select_get_file_list(flags,space,iter,flag,elem_size,maxseq,maxbytes,nseq,off,len) + unsigned flags; IN: Flags for extra information about operation + H5S_t *space; IN: Dataspace containing selection to use. + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + unsigned flag; IN: Flag to indicate whether to update the + iterator or not. + size_t elem_size; IN: Size of an element + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxbytes; IN: Maximum number of bytes to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + hsize_t *off; OUT: Array of offsets + hsize_t *len; OUT: Array of lengths + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. Updating the iterator is controlled with the FLAG + parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +herr_t +H5S_select_get_seq_list(unsigned flags, const H5S_t *space,H5S_sel_iter_t *iter, + size_t elem_size, size_t maxseq, size_t maxbytes, size_t *nseq, size_t *nbytes, + hsize_t *off, size_t *len) +{ + herr_t ret_value=SUCCEED; /* return value */ + + FUNC_ENTER_NOAPI (H5S_select_get_seq_list, FAIL); + + /* Check args */ + assert(space); + assert(iter); + assert(elem_size>0); + assert(maxseq>0); + assert(maxbytes>0); + assert(nseq); + assert(off); + assert(len); + + /* Get the list of sequences for each type selection */ /* [Defer (mostly) to the selection routines] */ switch(space->select.type) { - case H5S_SEL_POINTS: /* Sequence of points selected */ - ret_value=H5S_point_select_fill(fill,fill_size,space,buf); + case H5S_SEL_POINTS: /* Sequence of points selected */ + ret_value=H5S_point_select_get_seq_list(flags,space,iter,elem_size,maxseq,maxbytes,nseq,nbytes,off,len); break; - case H5S_SEL_HYPERSLABS: /* Hyperslab selection defined */ - ret_value=H5S_hyper_select_fill(fill,fill_size,space,buf); + case H5S_SEL_HYPERSLABS: /* Hyperslab selection defined */ + ret_value=H5S_hyper_select_get_seq_list(flags,space,iter,elem_size,maxseq,maxbytes,nseq,nbytes,off,len); break; - case H5S_SEL_ALL: /* Entire extent selected */ - ret_value=H5S_all_select_fill(fill,fill_size,space,buf); + case H5S_SEL_ALL: /* Entire extent selected */ + ret_value=H5S_all_select_get_seq_list(flags,space,iter,elem_size,maxseq,maxbytes,nseq,nbytes,off,len); break; - case H5S_SEL_NONE: /* Nothing selected */ - ret_value=SUCCEED; + case H5S_SEL_NONE: /* Nothing selected */ + *nseq=0; /* Set the number of sequences generated */ break; case H5S_SEL_ERROR: @@ -1608,10 +1910,891 @@ H5S_select_fill(void *_fill, size_t fill_size, const H5S_t *space, void *buf) break; } /* end switch */ +#ifdef LATER done: - if(_fill==NULL && fill) - H5MM_xfree(fill); +#endif /* LATER */ + FUNC_LEAVE (ret_value); +} /* H5S_select_get_seq_list() */ + +/*------------------------------------------------------------------------- + * Function: H5S_select_favail + * + * Purpose: Figure out the optimal number of elements to transfer to/from + * the file. + * + * Return: non-negative number of elements on success, zero on + * failure. + * + * Programmer: Quincey Koziol + * Wednesday, July 24, 2002 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +hsize_t +H5S_select_favail(const H5S_t *space, const H5S_sel_iter_t *iter, hsize_t max) +{ + hsize_t ret_value=0; /* Return value */ + + FUNC_ENTER_NOAPI (H5S_select_favail, 0); + + /* Check args */ + assert(space); + assert(iter); + assert(max>0); + + /* Get the number of elements to transfer for each type of selection */ + /* [Defer (mostly) to the selection routines] */ + switch(space->select.type) { + case H5S_SEL_POINTS: /* Sequence of points selected */ + ret_value=H5S_point_favail(space,iter,max); + break; + + case H5S_SEL_HYPERSLABS: /* Hyperslab selection defined */ + ret_value=H5S_hyper_favail(space,iter,max); + break; + + case H5S_SEL_ALL: /* Entire extent selected */ + ret_value=H5S_all_favail(space,iter,max); + break; + + case H5S_SEL_NONE: /* Nothing selected */ + ret_value=0; /* Set the number of elements to transfer */ + break; + + case H5S_SEL_ERROR: + case H5S_SEL_N: + assert(0 && "Invalid selection type!"); + break; + } /* end switch */ + +#ifdef LATER +done: +#endif /* LATER */ FUNC_LEAVE (ret_value); -} /* H5S_select_fill() */ +} /* H5S_select_favail() */ + + +/*------------------------------------------------------------------------- + * Function: H5S_select_fscat + * + * Purpose: Scatters dataset elements from the type conversion buffer BUF + * to the file F where the data points are arranged according to + * the file data space FILE_SPACE and stored according to + * LAYOUT and EFL. Each element is ELMT_SIZE bytes. + * The caller is requesting that NELMTS elements are copied. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Thursday, June 20, 2002 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5S_select_fscat (H5F_t *f, const struct H5O_layout_t *layout, + H5P_genplist_t *dc_plist, size_t elmt_size, + const H5S_t *file_space, H5S_sel_iter_t *file_iter, + hsize_t nelmts, hid_t dxpl_id, const void *_buf) +{ + const uint8_t *buf=_buf; /* Alias for pointer arithmetic */ + hsize_t *off=NULL; /* Array to store sequence offsets */ + size_t *len=NULL; /* Array to store sequence lengths */ + size_t vector_size; /* Value for vector size */ + size_t maxbytes; /* Number of bytes in the buffer */ + size_t nseq; /* Number of sequences generated */ + size_t nbytes; /* Number of bytes used in sequences */ + H5P_genplist_t *dx_plist; /* Dataset transfer property list */ + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5S_select_fscat, FAIL); + + /* Check args */ + assert (f); + assert (layout); + assert (elmt_size>0); + assert (file_space); + assert (file_iter); + assert (nelmts>0); + assert (_buf); + + /* Get the hyperslab vector size */ + if(TRUE!=H5P_isa_class(dxpl_id,H5P_DATASET_XFER) || NULL == (dx_plist = H5I_object(dxpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file access property list"); + if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value"); + + /* Allocate the vector I/O arrays */ + if((len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); + if((off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); + + /* Compute the number of bytes available in buffer */ + H5_ASSIGN_OVERFLOW(maxbytes,nelmts*elmt_size,hsize_t,size_t); + + /* Loop until all elements are written */ + while(maxbytes>0) { + /* Get list of sequences for selection to write */ + if(H5S_select_get_seq_list(H5S_GET_SEQ_LIST_SORTED,file_space,file_iter,elmt_size,vector_size,maxbytes,&nseq,&nbytes,off,len)<0) + HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); + + /* Write sequence list out */ + if (H5F_seq_writev(f, dxpl_id, layout, dc_plist, file_space, elmt_size, nseq, len, off, buf)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); + + /* Update buffer */ + buf += nbytes; + + /* Decrement number of elements left to process */ + assert(nbytes%elmt_size==0); + maxbytes -= nbytes; + } /* end while */ + +done: + if(len!=NULL) + H5FL_ARR_FREE(size_t,len); + if(off!=NULL) + H5FL_ARR_FREE(hsize_t,off); + FUNC_LEAVE (ret_value); +} /* H5S_select_fscat() */ + + +/*------------------------------------------------------------------------- + * Function: H5S_select_fgath + * + * Purpose: Gathers data points from file F and accumulates them in the + * type conversion buffer BUF. The LAYOUT argument describes + * how the data is stored on disk and EFL describes how the data + * is organized in external files. ELMT_SIZE is the size in + * bytes of a datum which this function treats as opaque. + * FILE_SPACE describes the data space of the dataset on disk + * and the elements that have been selected for reading (via + * hyperslab, etc). This function will copy at most NELMTS + * elements. + * + * Return: Success: Number of elements copied. + * Failure: 0 + * + * Programmer: Quincey Koziol + * Monday, June 24, 2002 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +hsize_t +H5S_select_fgath (H5F_t *f, const struct H5O_layout_t *layout, + H5P_genplist_t *dc_plist, + size_t elmt_size, const H5S_t *file_space, + H5S_sel_iter_t *file_iter, hsize_t nelmts, hid_t dxpl_id, + void *_buf/*out*/) +{ + uint8_t *buf=_buf; /* Alias for pointer arithmetic */ + hsize_t *off=NULL; /* Array to store sequence offsets */ + size_t *len=NULL; /* Array to store sequence lengths */ + size_t vector_size; /* Value for vector size */ + size_t maxbytes; /* Number of bytes in the buffer */ + size_t nseq; /* Number of sequences generated */ + size_t nbytes; /* Number of bytes used in sequences */ + H5P_genplist_t *dx_plist; /* Dataset transfer property list */ + hsize_t ret_value=nelmts; /* Return value */ + + FUNC_ENTER_NOAPI(H5S_select_fgath, 0); + + /* Check args */ + assert (f); + assert (layout); + assert (elmt_size>0); + assert (file_space); + assert (file_iter); + assert (nelmts>0); + assert (_buf); + + /* Get the hyperslab vector size */ + if(TRUE!=H5P_isa_class(dxpl_id,H5P_DATASET_XFER) || NULL == (dx_plist = H5I_object(dxpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a file access property list"); + if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, 0, "unable to get value"); + + /* Allocate the vector I/O arrays */ + if((len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O length vector array"); + if((off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O offset vector array"); + + /* Compute the number of bytes available in buffer */ + H5_ASSIGN_OVERFLOW(maxbytes,nelmts*elmt_size,hsize_t,size_t); + + /* Loop until all elements are written */ + while(maxbytes>0) { + /* Get list of sequences for selection to write */ + if(H5S_select_get_seq_list(H5S_GET_SEQ_LIST_SORTED,file_space,file_iter,elmt_size,vector_size,maxbytes,&nseq,&nbytes,off,len)<0) + HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed"); + + /* Read sequence list in */ + if (H5F_seq_readv(f, dxpl_id, layout, dc_plist, file_space, elmt_size, nseq, len, off, buf)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); + + /* Update buffer */ + buf += nbytes; + + /* Decrement number of elements left to process */ + assert(nbytes%elmt_size==0); + maxbytes -= nbytes; + } /* end while */ + +done: + if(len!=NULL) + H5FL_ARR_FREE(size_t,len); + if(off!=NULL) + H5FL_ARR_FREE(hsize_t,off); + FUNC_LEAVE (ret_value); +} /* H5S_select_fgath() */ + + +/*------------------------------------------------------------------------- + * Function: H5S_select_mscat + * + * Purpose: Scatters NELMTS data points from the scatter buffer + * TSCAT_BUF to the application buffer BUF. Each element is + * ELMT_SIZE bytes and they are organized in application memory + * according to SPACE. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Monday, July 8, 2002 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5S_select_mscat (const void *_tscat_buf, size_t elmt_size, const H5S_t *space, + H5S_sel_iter_t *iter, hsize_t nelmts, hid_t dxpl_id, void *_buf/*out*/) +{ + H5P_genplist_t *dx_plist; /* Dataset transfer property list */ + uint8_t *buf=(uint8_t *)_buf; /* Get local copies for address arithmetic */ + const uint8_t *tscat_buf=(const uint8_t *)_tscat_buf; + hsize_t *off=NULL; /* Array to store sequence offsets */ + size_t vector_size; /* Value for vector size */ + size_t *len=NULL; /* Array to store sequence lengths */ + size_t curr_len; /* Length of bytes left to process in sequence */ + size_t maxbytes; /* Number of bytes in the buffer */ + size_t nseq; /* Number of sequences generated */ + size_t curr_seq; /* Current sequence being processed */ + size_t nbytes; /* Number of bytes used in sequences */ + herr_t ret_value=SUCCEED; /* Number of elements scattered */ + + FUNC_ENTER_NOAPI(H5S_select_mscat, FAIL); + + /* Check args */ + assert (tscat_buf); + assert (elmt_size>0); + assert (space); + assert (iter); + assert (nelmts>0); + assert (buf); + + /* Get the hyperslab vector size */ + if(TRUE!=H5P_isa_class(dxpl_id,H5P_DATASET_XFER) || NULL == (dx_plist = H5I_object(dxpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list"); + if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value"); + + /* Allocate the vector I/O arrays */ + if((len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); + if((off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); + + /* Compute the number of bytes available in buffer */ + H5_ASSIGN_OVERFLOW(maxbytes,nelmts*elmt_size,hsize_t,size_t); + + /* Loop until all elements are written */ + while(maxbytes>0) { + /* Get list of sequences for selection to write */ + if(H5S_select_get_seq_list(0,space,iter,elmt_size,vector_size,maxbytes,&nseq,&nbytes,off,len)<0) + HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed"); + + /* Loop, while sequences left to process */ + for(curr_seq=0; curr_seq<nseq; curr_seq++) { + /* Get the number of bytes in sequence */ + curr_len=len[curr_seq]; + + HDmemcpy(buf+off[curr_seq],tscat_buf,curr_len); + + /* Advance offset in destination buffer */ + tscat_buf+=curr_len; + } /* end for */ + + /* Decrement number of elements left to process */ + assert(nbytes%elmt_size==0); + maxbytes -= nbytes; + } /* end while */ + +done: + if(len!=NULL) + H5FL_ARR_FREE(size_t,len); + if(off!=NULL) + H5FL_ARR_FREE(hsize_t,off); + FUNC_LEAVE(ret_value); +} /* H5S_select_mscat() */ + + +/*------------------------------------------------------------------------- + * Function: H5S_select_mgath + * + * Purpose: Gathers dataset elements from application memory BUF and + * copies them into the gather buffer TGATH_BUF. + * Each element is ELMT_SIZE bytes and arranged in application + * memory according to SPACE. + * The caller is requesting that at most NELMTS be gathered. + * + * Return: Success: Number of elements copied. + * Failure: 0 + * + * Programmer: Quincey Koziol + * Monday, June 24, 2002 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +hsize_t +H5S_select_mgath (const void *_buf, size_t elmt_size, const H5S_t *space, + H5S_sel_iter_t *iter, hsize_t nelmts, hid_t dxpl_id, void *_tgath_buf/*out*/) +{ + H5P_genplist_t *dx_plist; /* Dataset transfer property list */ + const uint8_t *buf=(const uint8_t *)_buf; /* Get local copies for address arithmetic */ + uint8_t *tgath_buf=(uint8_t *)_tgath_buf; + hsize_t *off=NULL; /* Array to store sequence offsets */ + size_t vector_size; /* Value for vector size */ + size_t *len=NULL; /* Array to store sequence lengths */ + size_t curr_len; /* Length of bytes left to process in sequence */ + size_t maxbytes; /* Number of bytes in the buffer */ + size_t nseq; /* Number of sequences generated */ + size_t curr_seq; /* Current sequence being processed */ + size_t nbytes; /* Number of bytes used in sequences */ + hsize_t ret_value=nelmts; /* Number of elements gathered */ + + FUNC_ENTER_NOAPI(H5S_select_mgath, 0); + + /* Check args */ + assert (buf); + assert (elmt_size>0); + assert (space); + assert (iter); + assert (nelmts>0); + assert (tgath_buf); + + /* Get the hyperslab vector size */ + if(TRUE!=H5P_isa_class(dxpl_id,H5P_DATASET_XFER) || NULL == (dx_plist = H5I_object(dxpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset transfer property list"); + if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, 0, "unable to get value"); + + /* Allocate the vector I/O arrays */ + if((len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O length vector array"); + if((off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O offset vector array"); + + /* Compute the number of bytes available in buffer */ + H5_ASSIGN_OVERFLOW(maxbytes,nelmts*elmt_size,hsize_t,size_t); + + /* Loop until all elements are written */ + while(maxbytes>0) { + /* Get list of sequences for selection to write */ + if(H5S_select_get_seq_list(0,space,iter,elmt_size,vector_size,maxbytes,&nseq,&nbytes,off,len)<0) + HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed"); + + /* Loop, while sequences left to process */ + for(curr_seq=0; curr_seq<nseq; curr_seq++) { + /* Get the number of bytes in sequence */ + curr_len=len[curr_seq]; + + HDmemcpy(tgath_buf,buf+off[curr_seq],curr_len); + + /* Advance offset in gather buffer */ + tgath_buf+=curr_len; + } /* end for */ + + /* Decrement number of elements left to process */ + assert(nbytes%elmt_size==0); + maxbytes -= nbytes; + } /* end while */ + +done: + if(len!=NULL) + H5FL_ARR_FREE(size_t,len); + if(off!=NULL) + H5FL_ARR_FREE(hsize_t,off); + FUNC_LEAVE(ret_value); +} /* H5S_select_mgath() */ + + +/*------------------------------------------------------------------------- + * Function: H5S_select_read + * + * Purpose: Reads directly from file into application memory. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Tuesday, July 23, 2002 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5S_select_read(H5F_t *f, const H5O_layout_t *layout, H5P_genplist_t *dc_plist, + size_t elmt_size, const H5S_t *file_space, + const H5S_t *mem_space, hid_t dxpl_id, void *_buf/*out*/) +{ + H5P_genplist_t *dx_plist; /* Dataset transfer property list */ + H5S_sel_iter_t *mem_iter=NULL; /* Memory selection iteration info */ + H5S_sel_iter_t *file_iter=NULL; /* File selection iteration info */ + uint8_t *buf; /* Local buffer pointer, for address arithmetic */ + hsize_t *mem_off=NULL; /* Array to store sequence offsets in memory */ + hsize_t *file_off=NULL; /* Array to store sequence offsets in the file */ + size_t vector_size; /* Value for vector size */ + size_t *mem_len=NULL; /* Array to store sequence lengths in memory */ + size_t *file_len=NULL; /* Array to store sequence lengths in the file */ + size_t maxbytes; /* Number of bytes in selection */ + size_t mem_nseq; /* Number of sequences generated in the file */ + size_t file_nseq; /* Number of sequences generated in memory */ + size_t mem_nbytes; /* Number of bytes used in memory sequences */ + size_t file_nbytes; /* Number of bytes used in file sequences */ + size_t curr_mem_seq; /* Current memory sequence to operate on */ + size_t curr_file_seq; /* Current file sequence to operate on */ + size_t tmp_file_len; /* Temporary number of bytes in file sequence */ + unsigned partial_file; /* Whether a partial file sequence was accessed */ + size_t orig_file_len; /* Original file sequence length for partial file access */ + size_t orig_file_seq; /* Original file sequence to operate on */ + size_t tot_file_seq; /* Number of file sequences to access */ + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5S_select_read, FAIL); + + /* Get the hyperslab vector size */ + if(TRUE!=H5P_isa_class(dxpl_id,H5P_DATASET_XFER) || NULL == (dx_plist = H5I_object(dxpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list"); + if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value"); + + /* Allocate the vector I/O arrays */ + if((mem_len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); + if((mem_off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); + if((file_len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); + if((file_off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); + + /* Allocate file iterator */ + if((file_iter = H5FL_ALLOC(H5S_sel_iter_t,1))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate selection iterator"); + + /* Initialize file iterator */ + if (H5S_select_iter_init(file_space, elmt_size, file_iter)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); + + /* Allocate memory iterator */ + if((mem_iter = H5FL_ALLOC(H5S_sel_iter_t,1))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate selection iterator"); + + /* Initialize memory iterator */ + if (H5S_select_iter_init(mem_space, elmt_size, mem_iter)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); + + /* Get number of bytes in selection */ + maxbytes=H5S_get_select_npoints(file_space)*elmt_size; + + /* Initialize sequence counts */ + curr_mem_seq=curr_file_seq=0; + mem_nseq=file_nseq=0; + + /* Loop, until all bytes are processed */ + while(maxbytes>0) { + /* Check if more file sequences are needed */ + if(curr_file_seq>=file_nseq) { + /* Get sequences for file selection */ + if(H5S_select_get_seq_list(H5S_GET_SEQ_LIST_SORTED,file_space,file_iter,elmt_size,vector_size,maxbytes,&file_nseq,&file_nbytes,file_off,file_len)<0) + HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); + + /* Start at the beginning of the sequences again */ + curr_file_seq=0; + } /* end if */ + + /* Check if more memory sequences are needed */ + if(curr_mem_seq>=mem_nseq) { + /* Get sequences for memory selection */ + if(H5S_select_get_seq_list(0,mem_space,mem_iter,elmt_size,vector_size,maxbytes,&mem_nseq,&mem_nbytes,mem_off,mem_len)<0) + HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); + + /* Start at the beginning of the sequences again */ + curr_mem_seq=0; + + /* Set the buffer pointer using the first sequence */ + H5_CHECK_OVERFLOW(mem_off[0],hsize_t,size_t); + buf=(uint8_t *)_buf+(size_t)mem_off[0]; + } /* end if */ + + /* Check if current file sequence will fit into current memory sequence */ + if(mem_len[curr_mem_seq]>=file_len[curr_file_seq]) { + /* Save the current number file sequence */ + orig_file_seq=curr_file_seq; + + /* Determine how many file sequences will fit into current memory sequence */ + tmp_file_len=0; + tot_file_seq=0; + while((tmp_file_len+file_len[curr_file_seq])<=mem_len[curr_mem_seq] && curr_file_seq<file_nseq) { + tmp_file_len+=file_len[curr_file_seq]; + curr_file_seq++; + tot_file_seq++; + } /* end while */ + + /* Check for partial file sequence */ + if(tmp_file_len<mem_len[curr_mem_seq] && curr_file_seq<file_nseq) { + /* Get the original file sequence length */ + orig_file_len=file_len[curr_file_seq]; + + /* Make the last file sequence a partial access */ + file_len[curr_file_seq]=mem_len[curr_mem_seq]-tmp_file_len; + + /* Increase the number of bytes to access */ + tmp_file_len=mem_len[curr_mem_seq]; + + /* Indicate that there is an extra sequence to include in the file access */ + tot_file_seq++; + + /* Indicate a partial file sequence */ + partial_file=1; + } /* end if */ + else + partial_file=0; + + /* Read file sequences into current memory sequence */ + if (H5F_seq_readv(f, dxpl_id, layout, dc_plist, file_space, elmt_size, tot_file_seq, &file_len[orig_file_seq], &file_off[orig_file_seq], buf)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error"); + + /* Update last file sequence, if it was partially accessed */ + if(partial_file) { + file_off[curr_file_seq]+=orig_file_len-file_len[curr_file_seq]; + file_len[curr_file_seq]=orig_file_len-file_len[curr_file_seq]; + } /* end if */ + + /* Check if the current memory sequence was only partially accessed */ + if(tmp_file_len<mem_len[curr_mem_seq]) { + /* Adjust current memory sequence */ + mem_off[curr_mem_seq]+=tmp_file_len; + mem_len[curr_mem_seq]-=tmp_file_len; + + /* Adjust memory buffer pointer */ + buf+=tmp_file_len; + } /* end if */ + else { + /* Must have used entire memory sequence, advance to next one */ + curr_mem_seq++; + + /* Check if it is valid to adjust buffer pointer */ + if(curr_mem_seq<mem_nseq) { + H5_CHECK_OVERFLOW(mem_off[curr_mem_seq],hsize_t,size_t); + buf=(uint8_t *)_buf+(size_t)mem_off[curr_mem_seq]; + } /* end if */ + } /* end else */ + + /* Decrement number of bytes left to process */ + maxbytes-=tmp_file_len; + } /* end if */ + else { + /* Save number of bytes to access */ + tmp_file_len=mem_len[curr_mem_seq]; + + /* Read part of current file sequence into current memory sequence */ + if (H5F_seq_read(f, dxpl_id, layout, dc_plist, file_space, elmt_size, tmp_file_len, file_off[curr_file_seq], buf)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error"); + + /* Update current file sequence information */ + file_off[curr_file_seq]+=tmp_file_len; + file_len[curr_file_seq]-=tmp_file_len; + + /* Increment memory sequence */ + curr_mem_seq++; + + /* Check if it is valid to adjust buffer pointer */ + if(curr_mem_seq<mem_nseq) { + H5_CHECK_OVERFLOW(mem_off[curr_mem_seq],hsize_t,size_t); + buf=(uint8_t *)_buf+(size_t)mem_off[curr_mem_seq]; + } /* end if */ + + /* Decrement number of bytes left to process */ + maxbytes-=tmp_file_len; + } /* end else */ + } /* end while */ + +done: + /* Release file selection iterator */ + if(file_iter!=NULL) { + if (H5S_sel_iter_release(file_space, file_iter)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); + H5FL_FREE(H5S_sel_iter_t,file_iter); + } /* end if */ + + /* Release memory selection iterator */ + if(mem_iter!=NULL) { + if (H5S_sel_iter_release(mem_space, mem_iter)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); + H5FL_FREE(H5S_sel_iter_t,mem_iter); + } /* end if */ + + /* Free vector arrays */ + if(file_len!=NULL) + H5FL_ARR_FREE(size_t,file_len); + if(file_off!=NULL) + H5FL_ARR_FREE(hsize_t,file_off); + if(mem_len!=NULL) + H5FL_ARR_FREE(size_t,mem_len); + if(mem_off!=NULL) + H5FL_ARR_FREE(hsize_t,mem_off); + FUNC_LEAVE(ret_value); +} /* end H5S_select_read() */ + + +/*------------------------------------------------------------------------- + * Function: H5S_select_write + * + * Purpose: Writes directly from application memory into a file + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Tuesday, July 23, 2002 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5S_select_write(H5F_t *f, const H5O_layout_t *layout, H5P_genplist_t *dc_plist, + size_t elmt_size, const H5S_t *file_space, + const H5S_t *mem_space, hid_t dxpl_id, const void *_buf/*out*/) +{ + H5P_genplist_t *dx_plist; /* Dataset transfer property list */ + H5S_sel_iter_t *mem_iter=NULL; /* Memory selection iteration info */ + H5S_sel_iter_t *file_iter=NULL; /* File selection iteration info */ + const uint8_t *buf; /* Local buffer pointer, for address arithmetic */ + hsize_t *mem_off=NULL; /* Array to store sequence offsets in memory */ + hsize_t *file_off=NULL; /* Array to store sequence offsets in the file */ + size_t vector_size; /* Value for vector size */ + size_t *mem_len=NULL; /* Array to store sequence lengths in memory */ + size_t *file_len=NULL; /* Array to store sequence lengths in the file */ + size_t maxbytes; /* Number of bytes in selection */ + size_t mem_nseq; /* Number of sequences generated in the file */ + size_t file_nseq; /* Number of sequences generated in memory */ + size_t mem_nbytes; /* Number of bytes used in memory sequences */ + size_t file_nbytes; /* Number of bytes used in file sequences */ + size_t curr_mem_seq; /* Current memory sequence to operate on */ + size_t curr_file_seq; /* Current file sequence to operate on */ + size_t tmp_file_len; /* Temporary number of bytes in file sequence */ + unsigned partial_file; /* Whether a partial file sequence was accessed */ + size_t orig_file_len; /* Original file sequence length for partial file access */ + size_t orig_file_seq; /* Original file sequence to operate on */ + size_t tot_file_seq; /* Number of file sequences to access */ + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5S_select_write, FAIL); + + /* Get the hyperslab vector size */ + if(TRUE!=H5P_isa_class(dxpl_id,H5P_DATASET_XFER) || NULL == (dx_plist = H5I_object(dxpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list"); + if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value"); + + /* Allocate the vector I/O arrays */ + if((mem_len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); + if((mem_off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); + if((file_len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); + if((file_off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); + + /* Allocate file iterator */ + if((file_iter = H5FL_ALLOC(H5S_sel_iter_t,1))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate selection iterator"); + + /* Initialize file iterator */ + if (H5S_select_iter_init(file_space, elmt_size, file_iter)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); + + /* Allocate memory iterator */ + if((mem_iter = H5FL_ALLOC(H5S_sel_iter_t,1))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate selection iterator"); + + /* Initialize memory iterator */ + if (H5S_select_iter_init(mem_space, elmt_size, mem_iter)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); + + /* Get number of bytes in selection */ + maxbytes=H5S_get_select_npoints(file_space)*elmt_size; + + /* Initialize sequence counts */ + curr_mem_seq=curr_file_seq=0; + mem_nseq=file_nseq=0; + + /* Loop, until all bytes are processed */ + while(maxbytes>0) { + /* Check if more file sequences are needed */ + if(curr_file_seq>=file_nseq) { + /* Get sequences for file selection */ + if(H5S_select_get_seq_list(H5S_GET_SEQ_LIST_SORTED,file_space,file_iter,elmt_size,vector_size,maxbytes,&file_nseq,&file_nbytes,file_off,file_len)<0) + HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); + + /* Start at the beginning of the sequences again */ + curr_file_seq=0; + } /* end if */ + + /* Check if more memory sequences are needed */ + if(curr_mem_seq>=mem_nseq) { + /* Get sequences for memory selection */ + if(H5S_select_get_seq_list(0,mem_space,mem_iter,elmt_size,vector_size,maxbytes,&mem_nseq,&mem_nbytes,mem_off,mem_len)<0) + HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); + + /* Start at the beginning of the sequences again */ + curr_mem_seq=0; + + /* Set the buffer pointer using the first sequence */ + H5_CHECK_OVERFLOW(mem_off[0],hsize_t,size_t); + buf=(const uint8_t *)_buf+(size_t)mem_off[0]; + } /* end if */ + + /* Check if current file sequence will fit into current memory sequence */ + if(mem_len[curr_mem_seq]>=file_len[curr_file_seq]) { + /* Save the current number file sequence */ + orig_file_seq=curr_file_seq; + + /* Determine how many file sequences will fit into current memory sequence */ + tmp_file_len=0; + tot_file_seq=0; + while((tmp_file_len+file_len[curr_file_seq])<=mem_len[curr_mem_seq] && curr_file_seq<file_nseq) { + tmp_file_len+=file_len[curr_file_seq]; + curr_file_seq++; + tot_file_seq++; + } /* end while */ + + /* Check for partial file sequence */ + if(tmp_file_len<mem_len[curr_mem_seq] && curr_file_seq<file_nseq) { + /* Get the original file sequence length */ + orig_file_len=file_len[curr_file_seq]; + + /* Make the last file sequence a partial access */ + file_len[curr_file_seq]=mem_len[curr_mem_seq]-tmp_file_len; + + /* Increase the number of bytes to access */ + tmp_file_len=mem_len[curr_mem_seq]; + + /* Indicate that there is an extra sequence to include in the file access */ + tot_file_seq++; + + /* Indicate a partial file sequence */ + partial_file=1; + } /* end if */ + else + partial_file=0; + + /* Write current memory sequence into file sequences */ + if (H5F_seq_writev(f, dxpl_id, layout, dc_plist, file_space, elmt_size, tot_file_seq, &file_len[orig_file_seq], &file_off[orig_file_seq], buf)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); + + /* Update last file sequence, if it was partially accessed */ + if(partial_file) { + file_off[curr_file_seq]+=orig_file_len-file_len[curr_file_seq]; + file_len[curr_file_seq]=orig_file_len-file_len[curr_file_seq]; + } /* end if */ + + /* Check if the current memory sequence was only partially accessed */ + if(tmp_file_len<mem_len[curr_mem_seq]) { + /* Adjust current memory sequence */ + mem_off[curr_mem_seq]+=tmp_file_len; + mem_len[curr_mem_seq]-=tmp_file_len; + + /* Adjust memory buffer pointer */ + buf+=tmp_file_len; + } /* end if */ + else { + /* Must have used entire memory sequence, advance to next one */ + curr_mem_seq++; + + /* Check if it is valid to adjust buffer pointer */ + if(curr_mem_seq<mem_nseq) { + H5_CHECK_OVERFLOW(mem_off[curr_mem_seq],hsize_t,size_t); + buf=(const uint8_t *)_buf+(size_t)mem_off[curr_mem_seq]; + } /* end if */ + } /* end else */ + + /* Decrement number of bytes left to process */ + maxbytes-=tmp_file_len; + } /* end if */ + else { + /* Save number of bytes to access */ + tmp_file_len=mem_len[curr_mem_seq]; + + /* Write part of current memory sequence to current file sequence */ + if (H5F_seq_write(f, dxpl_id, layout, dc_plist, file_space, elmt_size, tmp_file_len, file_off[curr_file_seq], buf)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); + + /* Update current file sequence information */ + file_off[curr_file_seq]+=tmp_file_len; + file_len[curr_file_seq]-=tmp_file_len; + + /* Increment memory sequence */ + curr_mem_seq++; + + /* Check if it is valid to adjust buffer pointer */ + if(curr_mem_seq<mem_nseq) { + H5_CHECK_OVERFLOW(mem_off[curr_mem_seq],hsize_t,size_t); + buf=(const uint8_t *)_buf+(size_t)mem_off[curr_mem_seq]; + } /* end if */ + + /* Decrement number of bytes left to process */ + maxbytes-=tmp_file_len; + } /* end else */ + } /* end while */ + +done: + /* Release file selection iterator */ + if(file_iter!=NULL) { + if (H5S_sel_iter_release(file_space, file_iter)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); + H5FL_FREE(H5S_sel_iter_t,file_iter); + } /* end if */ + + /* Release memory selection iterator */ + if(mem_iter!=NULL) { + if (H5S_sel_iter_release(mem_space, mem_iter)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); + H5FL_FREE(H5S_sel_iter_t,mem_iter); + } /* end if */ + + /* Free vector arrays */ + if(file_len!=NULL) + H5FL_ARR_FREE(size_t,file_len); + if(file_off!=NULL) + H5FL_ARR_FREE(hsize_t,file_off); + if(mem_len!=NULL) + H5FL_ARR_FREE(size_t,mem_len); + if(mem_off!=NULL) + H5FL_ARR_FREE(hsize_t,mem_off); + FUNC_LEAVE(ret_value); +} /* end H5S_select_write() */ diff --git a/src/H5Tconv.c b/src/H5Tconv.c index e61e2cb..beeb7bf 100644 --- a/src/H5Tconv.c +++ b/src/H5Tconv.c @@ -2372,8 +2372,11 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts, } /* end if */ /* If the sequence gets shorter, pad out the original sequence with zeros */ - if(bg_seq_len<seq_len) - HDmemset((uint8_t *)tmp_buf+dst_base_size*bg_seq_len,0,(seq_len-bg_seq_len)*dst_base_size); + H5_CHECK_OVERFLOW(bg_seq_len,hsize_t,hssize_t); + if((hssize_t)bg_seq_len<seq_len) { + H5_CHECK_OVERFLOW((seq_len-bg_seq_len),hsize_t,size_t); + HDmemset((uint8_t *)tmp_buf+dst_base_size*bg_seq_len,0,(size_t)(seq_len-bg_seq_len)*dst_base_size); + } /* end if */ } /* end if */ /* Convert VL sequence */ @@ -2388,7 +2391,8 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts, "can't write VL data"); /* For nested VL case, free leftover heap objects from the deeper level if the length of new data elements is shorted than the old data elements.*/ - if(nested && seq_len<bg_seq_len) { + H5_CHECK_OVERFLOW(bg_seq_len,hsize_t,hssize_t); + if(nested && seq_len<(hssize_t)bg_seq_len) { uint8_t *tmp_p=tmp_buf; tmp_p += seq_len*dst_base_size; for(i=0; i<(bg_seq_len-seq_len); i++) { |